A new change just went live that excludes + and - when copying the contents of a diff. That feature of the plugin shouldn't be needed now.
Could this be the cause of missing letters at the start of each line in diffs?
https://github.com/scala/scala.epfl.ch/commit/d8fcdfab9a2adf2d6cfe5e10979ba034cf38bf47

EDIT: confirmed, that was it
Also having this issue, you can disable the feature while we wait for it to be removed:
remove-diff-signs

FYI: GitHub disabled this a little while ago after a report of the first character missing on twitter. Looks like the person was using Refined GitHub based on their screen shot. Not sure when it'll be turned back on though.
Jolly annoying!

The fix from @evanmcmahonf works a treat!
Latest solution by @KattMingMing in #1451.
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Also having this issue, you can disable the feature while we wait for it to be removed:
remove-diff-signs