When I try to go over recent changes, the list looks like this for me:

It appears not to be sorted by anything meaningful. It's not sorted by date, not by size of the document (not that this would make sense).
The Version in use is 0.5.1, running on MySQL.
on HackMD.io it does _not_ seem to be a problem. Perhaps it has either been fixed already, or this is a problem specific to MySQL?
It seems to be no problem on my 0.5.1 instance with PostgreSQL backend either. Let's check the source code.
The sources do request ordering:
https://github.com/hackmdio/hackmd/blob/a99cac0cf05acaddd38f21851e85ae542ebc0070/lib/models/revision.js#L108-L159
There are two things I can think of: We do it wrong and it's ignored. Or there is a function hidden somewhere I haven't found in the last 5 minutes.
The docs say this: https://sequelize.readthedocs.io/en/v3/docs/querying/#ordering
Maybe the additional quotes are a problem:
Needs some work and testing.
I just curl'd the revisions url, to make sure the client does not do weird things. It does not. The weird ordering is offeref by my server.
curl "https://myserver/pad-id/revision" -H "Host: myserver" -H "Cookie: connect.sid=redacted"
Response
(numbers and line endings slightly formatted for readability, and with added comments from me)
{"revision":[
{"time":1_496_081_393_000,"length":21898}, // pretty high timestamp
{"time":1_485_865_749_000,"length":12908}, // older one
{"time":1_483_606_477_000,"length":3974}, // even older one, maybe this is descending?
{"time":1_493_372_736_000,"length":19782}, // huh? higher?
{"time":1_490_471_561_000,"length":18313}, // falling
{"time":1_483_576_776_000,"length":3229}, // falling
{"time":1_483_571_376_000,"length":2187}, // falling
{"time":1_483_600_519_000,"length":3235}, // higher once again.
{"time":1_484_412_746_000,"length":6419}, // even higher than the last.
{"time":1_485_620_088_000,"length":10594}, // rising once more
{"time":1_492_767_780_000,"length":19734}, // still rising
{"time":1_484_178_545_000,"length":5667}, // lower
{"time":1_489_399_174_000,"length":15421}, // higher
{"time":1_485_941_469_000,"length":13587}, // lower
{"time":1_489_398_575_000,"length":15378}, // no apparent pattern.
{"time":1_485_940_869_000,"length":13549},
{"time":1_483_576_176_000,"length":3048},
{"time":1_490_569_065_000,"length":19019},
{"time":1_484_192_945_000,"length":6032},
{"time":1_495_193_479_000,"length":21595},
{"time":1_483_826_978_000,"length":5156},
{"time":1_487_627_216_000,"length":15280},
{"time":1_490_011_476_000,"length":16063},
{"time":1_485_521_389_000,"length":8275},
{"time":1_483_607_076_000,"length":3975},
{"time":1_490_460_171_000,"length":18047},
{"time":1_487_613_717_000,"length":14972},
{"time":1_485_869_650_000,"length":13163},
{"time":1_484_403_746_000,"length":6391},
{"time":1_487_335_327_000,"length":14057},
{"time":1_495_474_880_000,"length":21716},
{"time":1_494_586_277_000,"length":20370},
{"time":1_495_475_480_000,"length":21722},
{"time":1_490_599_362_000,"length":19217},
{"time":1_483_827_578_000,"length":5213},
{"time":1_485_618_290_000,"length":9989},
{"time":1_490_570_262_000,"length":19122},
{"time":1_498_511_824_000,"length":21920},
{"time":1_484_404_346_000,"length":6415},
{"time":1_490_598_771_000,"length":19219},
{"time":1_485_532_788_000,"length":9985},
{"time":1_489_400_974_000,"length":16016},
{"time":1_495_477_580_000,"length":21853},
{"time":1_490_461_961_000,"length":18231},
{"time":1_485_532_188_000,"length":9772},
{"time":1_495_148_780_000,"length":21478},
{"time":1_484_222_546_000,"length":6208},
{"time":1_484_818_646_000,"length":7469},
{"time":1_490_010_877_000,"length":16014},
{"time":1_485_860_949_000,"length":11981},
{"time":1_484_827_947_000,"length":7552},
{"time":1_484_817_447_000,"length":7365},
{"time":1_492_777_680_000,"length":19769},
{"time":1_485_870_249_000,"length":13182},
{"time":1_494_584_178_000,"length":20120},
{"time":1_485_521_988_000,"length":8595},
{"time":1_494_227_299_000,"length":19915},
{"time":1_494_969_087_000,"length":20863},
{"time":1_483_540_476_000,"length":955},
{"time":1_487_347_915_000,"length":14583},
{"time":1_495_192_881_000,"length":21597},
{"time":1_485_523_788_000,"length":8650},
{"time":1_494_585_376_000,"length":20137},
{"time":1_485_637_489_000,"length":11090},
{"time":1_495_464_078_000,"length":21716},
{"time":1_485_942_669_000,"length":13605},
{"time":1_485_628_489_000,"length":10843},
{"time":1_485_861_549_000,"length":12562},
{"time":1_490_601_762_000,"length":19431},
{"time":1_492_499_302_000,"length":19432},
{"time":1_487_626_617_000,"length":15276},
{"time":1_483_658_076_000,"length":4233},
{"time":1_483_665_577_000,"length":4690},
{"time":1_483_548_276_000,"length":1361},
{"time":1_495_182_378_000,"length":21597},
{"time":1_483_538_777_000,"length":0},
{"time":1_490_012_978_000,"length":16267},
{"time":1_485_859_749_000,"length":11197},
{"time":1_493_668_236_000,"length":19808},
{"time":1_493_667_648_000,"length":19815},
{"time":1_487_627_816_000,"length":15206},
{"time":1_483_565_976_000,"length":1752},
{"time":1_485_860_349_000,"length":11369},
{"time":1_483_541_076_000,"length":1073},
{"time":1_495_456_878_000,"length":21694},
{"time":1_484_826_747_000,"length":7469},
{"time":1_494_973_295_000,"length":21165},
{"time":1_495_457_478_000,"length":21716},
{"time":1_484_190_545_000,"length":5924},
{"time":1_490_484_161_000,"length":18643},
{"time":1_487_613_125_000,"length":14738},
{"time":1_484_816_847_000,"length":7344},
{"time":1_485_523_188_000,"length":8646},
{"time":1_490_569_662_000,"length":19025},
{"time":1_487_336_215_000,"length":14190},
{"time":1_490_571_462_000,"length":19233},
{"time":1_495_023_393_000,"length":21307},
{"time":1_483_539_276_000,"length":292},
{"time":1_483_699_777_000,"length":4960},
{"time":1_494_588_376_000,"length":20564},
{"time":1_490_482_669_000,"length":18545},
{"time":1_485_283_648_000,"length":7693},
{"time":1_491_154_077_000,"length":19431},
{"time":1_490_012_077_000,"length":16176},
{"time":1_483_817_979_000,"length":5119},
{"time":1_483_573_776_000,"length":2307},
{"time":1_490_472_161_000,"length":18413},
{"time":1_483_699_178_000,"length":4690},
{"time":1_483_557_576_000,"length":1607},
{"time":1_483_574_376_000,"length":2479},
{"time":1_494_228_188_000,"length":19944},
{"time":1_492_775_580_000,"length":19767},
{"time":1_493_398_538_000,"length":19808},
{"time":1_484_124_579_000,"length":5481},
{"time":1_485_520_789_000,"length":8121},
{"time":1_489_400_374_000,"length":15886},
{"time":1_487_346_715_000,"length":14282},
{"time":1_483_666_176_000,"length":4690},
{"time":1_495_178_788_000,"length":21597},
{"time":1_485_854_951_000,"length":11197},
{"time":1_484_818_046_000,"length":7397},
{"time":1_487_347_392_000,"length":14453},
{"time":1_490_570_863_000,"length":19233},
{"time":1_487_614_316_000,"length":15101},
{"time":1_485_530_988_000,"length":8732},
{"time":1_484_816_248_000,"length":6752},
{"time":1_485_946_269_000,"length":13927},
{"time":1_487_624_217_000,"length":15106},
{"time":1_485_630_288_000,"length":10949},
{"time":1_490_601_162_000,"length":19297},
{"time":1_485_531_589_000,"length":9404},
{"time":1_485_945_669_000,"length":13706},
{"time":1_483_602_576_000,"length":3932},
{"time":1_483_574_976_000,"length":2521},
{"time":1_495_472_179_000,"length":21716},
{"time":1_485_870_850_000,"length":13537},
{"time":1_489_399_775_000,"length":15844},
{"time":1_485_629_088_000,"length":10921},
{"time":1_495_234_287_000,"length":21629},
{"time":1_484_409_746_000,"length":6419},
{"time":1_483_657_477_000,"length":4135},
{"time":1_490_600_562_000,"length":19247},
{"time":1_483_603_476_000,"length":3947},
{"time":1_485_953_169_000,"length":13993},
{"time":1_487_683_626_000,"length":15314},
{"time":1_485_283_048_000,"length":7641},
{"time":1_495_452_085_000,"length":21679},
{"time":1_485_940_270_000,"length":13549},
{"time":1_494_584_776_000,"length":20129},
{"time":1_484_216_546_000,"length":6074},
{"time":1_485_868_449_000,"length":13016},
{"time":1_495_149_378_000,"length":21589},
{"time":1_494_586_876_000,"length":20629},
{"time":1_495_089_089_000,"length":21307},
{"time":1_494_680_187_000,"length":20736},
{"time":1_483_656_876_000,"length":3952},
{"time":1_483_575_577_000,"length":2745},
{"time":1_490_567_569_000,"length":18964},
{"time":1_483_548_876_000,"length":1361},
{"time":1_485_869_049_000,"length":12965},
{"time":1_484_123_980_000,"length":5267},
{"time":1_485_865_149_000,"length":12860},
{"time":1_487_373_416_000,"length":14677},
{"time":1_485_522_588_000,"length":8598},
{"time":1_483_547_676_000,"length":1288},
{"time":1_494_672_988_000,"length":20564},
{"time":1_483_601_977_000,"length":3520},
{"time":1_485_284_247_000,"length":7838},
{"time":1_490_396_765_000,"length":16266},
{"time":1_485_867_849_000,"length":12998},
{"time":1_485_619_489_000,"length":10281},
{"time":1_483_570_776_000,"length":1800},
{"time":1_485_618_888_000,"length":10239},
{"time":1_494_973_964_000,"length":21124},
{"time":1_492_765_992_000,"length":19652},
{"time":1_494_680_776_000,"length":20868},
{"time":1_483_539_876_000,"length":476},
{"time":1_483_558_176_000,"length":1637},
{"time":1_485_620_689_000,"length":10749},
{"time":1_487_626_017_000,"length":15229},
{"time":1_484_248_646_000,"length":6293}
]}
Can you try to edit the mentioned section in the models and remove the quotation marks inside the order statement?
Should hurt anything but maybe fix the problem :D
JSON Output after the change
{"revision":[
{"time":1498511824000,"length":21920},
{"time":1496081393000,"length":21898},
{"time":1495477580000,"length":21853},
{"time":1495475480000,"length":21722},
{"time":1495474880000,"length":21716},
{"time":1495472179000,"length":21716},
{"time":1495464078000,"length":21716},
{"time":1495457478000,"length":21716},
{"time":1495456878000,"length":21694},
{"time":1495452085000,"length":21679},
{"time":1495234287000,"length":21629},
{"time":1495193479000,"length":21595},
{"time":1495192881000,"length":21597},
{"time":1495182378000,"length":21597},
{"time":1495178788000,"length":21597},
{"time":1495149378000,"length":21589},
{"time":1495148780000,"length":21478},
{"time":1495089089000,"length":21307},
{"time":1495023393000,"length":21307},
{"time":1494973964000,"length":21124},
{"time":1494973295000,"length":21165},
{"time":1494969087000,"length":20863},
{"time":1494680776000,"length":20868},
{"time":1494680187000,"length":20736},
{"time":1494672988000,"length":20564},
{"time":1494588376000,"length":20564},
{"time":1494586876000,"length":20629},
{"time":1494586277000,"length":20370},
{"time":1494585376000,"length":20137},
{"time":1494584776000,"length":20129},
{"time":1494584178000,"length":20120},
{"time":1494228188000,"length":19944},
{"time":1494227299000,"length":19915},
{"time":1493668236000,"length":19808},
{"time":1493667648000,"length":19815},
{"time":1493398538000,"length":19808},
{"time":1493372736000,"length":19782},
{"time":1492777680000,"length":19769},
{"time":1492775580000,"length":19767},
{"time":1492767780000,"length":19734},
{"time":1492765992000,"length":19652},
{"time":1492499302000,"length":19432},
{"time":1491154077000,"length":19431},
{"time":1490601762000,"length":19431},
{"time":1490601162000,"length":19297},
{"time":1490600562000,"length":19247},
{"time":1490599362000,"length":19217},
{"time":1490598771000,"length":19219},
{"time":1490571462000,"length":19233},
{"time":1490570863000,"length":19233},
{"time":1490570262000,"length":19122},
{"time":1490569662000,"length":19025},
{"time":1490569065000,"length":19019},
{"time":1490567569000,"length":18964},
{"time":1490484161000,"length":18643},
{"time":1490482669000,"length":18545},
{"time":1490472161000,"length":18413},
{"time":1490471561000,"length":18313},
{"time":1490461961000,"length":18231},
{"time":1490460171000,"length":18047},
{"time":1490396765000,"length":16266},
{"time":1490012978000,"length":16267},
{"time":1490012077000,"length":16176},
{"time":1490011476000,"length":16063},
{"time":1490010877000,"length":16014},
{"time":1489400974000,"length":16016},
{"time":1489400374000,"length":15886},
{"time":1489399775000,"length":15844},
{"time":1489399174000,"length":15421},
{"time":1489398575000,"length":15378},
{"time":1487683626000,"length":15314},
{"time":1487627816000,"length":15206},
{"time":1487627216000,"length":15280},
{"time":1487626617000,"length":15276},
{"time":1487626017000,"length":15229},
{"time":1487624217000,"length":15106},
{"time":1487614316000,"length":15101},
{"time":1487613717000,"length":14972},
{"time":1487613125000,"length":14738},
{"time":1487373416000,"length":14677},
{"time":1487347915000,"length":14583},
{"time":1487347392000,"length":14453},
{"time":1487346715000,"length":14282},
{"time":1487336215000,"length":14190},
{"time":1487335327000,"length":14057},
{"time":1485953169000,"length":13993},
{"time":1485946269000,"length":13927},
{"time":1485945669000,"length":13706},
{"time":1485942669000,"length":13605},
{"time":1485941469000,"length":13587},
{"time":1485940869000,"length":13549},
{"time":1485940270000,"length":13549},
{"time":1485870850000,"length":13537},
{"time":1485870249000,"length":13182},
{"time":1485869650000,"length":13163},
{"time":1485869049000,"length":12965},
{"time":1485868449000,"length":13016},
{"time":1485867849000,"length":12998},
{"time":1485865749000,"length":12908},
{"time":1485865149000,"length":12860},
{"time":1485861549000,"length":12562},
{"time":1485860949000,"length":11981},
{"time":1485860349000,"length":11369},
{"time":1485859749000,"length":11197},
{"time":1485854951000,"length":11197},
{"time":1485637489000,"length":11090},
{"time":1485630288000,"length":10949},
{"time":1485629088000,"length":10921},
{"time":1485628489000,"length":10843},
{"time":1485620689000,"length":10749},
{"time":1485620088000,"length":10594},
{"time":1485619489000,"length":10281},
{"time":1485618888000,"length":10239},
{"time":1485618290000,"length":9989},
{"time":1485532788000,"length":9985},
{"time":1485532188000,"length":9772},
{"time":1485531589000,"length":9404},
{"time":1485530988000,"length":8732},
{"time":1485523788000,"length":8650},
{"time":1485523188000,"length":8646},
{"time":1485522588000,"length":8598},
{"time":1485521988000,"length":8595},
{"time":1485521389000,"length":8275},
{"time":1485520789000,"length":8121},
{"time":1485284247000,"length":7838},
{"time":1485283648000,"length":7693},
{"time":1485283048000,"length":7641},
{"time":1484827947000,"length":7552},
{"time":1484826747000,"length":7469},
{"time":1484818646000,"length":7469},
{"time":1484818046000,"length":7397},
{"time":1484817447000,"length":7365},
{"time":1484816847000,"length":7344},
{"time":1484816248000,"length":6752},
{"time":1484412746000,"length":6419},
{"time":1484409746000,"length":6419},
{"time":1484404346000,"length":6415},
{"time":1484403746000,"length":6391},
{"time":1484248646000,"length":6293},
{"time":1484222546000,"length":6208},
{"time":1484216546000,"length":6074},
{"time":1484192945000,"length":6032},
{"time":1484190545000,"length":5924},
{"time":1484178545000,"length":5667},
{"time":1484124579000,"length":5481},
{"time":1484123980000,"length":5267},
{"time":1483827578000,"length":5213},
{"time":1483826978000,"length":5156},
{"time":1483817979000,"length":5119},
{"time":1483699777000,"length":4960},
{"time":1483699178000,"length":4690},
{"time":1483666176000,"length":4690},
{"time":1483665577000,"length":4690},
{"time":1483658076000,"length":4233},
{"time":1483657477000,"length":4135},
{"time":1483656876000,"length":3952},
{"time":1483607076000,"length":3975},
{"time":1483606477000,"length":3974},
{"time":1483603476000,"length":3947},
{"time":1483602576000,"length":3932},
{"time":1483601977000,"length":3520},
{"time":1483600519000,"length":3235},
{"time":1483576776000,"length":3229},
{"time":1483576176000,"length":3048},
{"time":1483575577000,"length":2745},
{"time":1483574976000,"length":2521},
{"time":1483574376000,"length":2479},
{"time":1483573776000,"length":2307},
{"time":1483571376000,"length":2187},
{"time":1483570776000,"length":1800},
{"time":1483565976000,"length":1752},
{"time":1483558176000,"length":1637},
{"time":1483557576000,"length":1607},
{"time":1483548876000,"length":1361},
{"time":1483548276000,"length":1361},
{"time":1483547676000,"length":1288},
{"time":1483541076000,"length":1073},
{"time":1483540476000,"length":955},
{"time":1483539876000,"length":476},
{"time":1483539276000,"length":292},
{"time":1483538777000,"length":0}
]}
Screenshot after the change

For some reason, the pull request did not link here. Here it is: #566
I think upgrade to Sequelize v4 would solve this issue.
But Sequelize v4 have more minor issues and sequelize-cli not support v4 yet.