Godot version: v3.1.1 stable win64
OS/device including version: Windows 10 64 bit version 1809
What i did: I tried to play around with the new tilemap system, especially because of the new autotile feature. I expected the tiles to be placed and rendered correctly but instead the bottom ones almost always glitch out.
Steps to reproduce: Start with a blank node called whatever, i used "World".
Then add a Node2D TileMap and create a new tile map.
Add your tilemap image and select your 3x3 set of tiles, mask the center parts so the parts will connect correctly.
Edit your tilemap and see the errors occuring.
Errors:

What i expect:


Possible extra information:



Minimal reproduction project:
Platformer Setup Test.zip
I don't know how this happened but your TileSet is corrupted. But you can fix it.
The bottom tiles have an invisible out of bounds sibling. To see them go to the Priority tab and click on one of the bottom tiles. Not only the tile you clicked on will be highlighted but also the one right below it although it is clearly out of bounds.
When you try to place the tiles Godot will choose a random tile with a fitting bitmask. As the oob tiles for some reasons have the same bitmask, there is a 50% chance you will place a corrupt bottom tile.
How to repair your tile set:
Yes, I clearly scaled the tilesector after creating a bitmask. The once that are outside never got scaled back so when i moved it, they got outside of the texture.
I hope someone can adjust it so that bitmasks outside the set don't count.
Had the same problem, @DavidSichma 's fix worked!
Just bad mask settings? Not a bug then...?
It should just ignore tiles outside the bounds of the tileset tough.
Would have fixed this wierd scaling issue. It is most certainly a bug since scaling shouldn't preserve data which doesn't exist.
I don't know if my problem is related but I experienced the following:
System: Linux PopOs 20.0.4 LTS
Godot: 3.2.3
I had created a tilemap with a tileset resource. Within the tileset resource I added a png spritesheet that was 192x96, and created two autotiles on it. I then modified the png in Aseprite (the program I originally created it; I modified the aseprite file and then exported the modified png to overwrite the original which was being used by the tileset.) After overwriting the png file I went back into Godot and into that tileset resource and removed the second autotile. I added 3 more autotiles (a 1x3, a 3x1, and another 3x3), as well as a single tile, and a 2x2 atlas tile. The modified png is larger than the 192x96 (it is now 224x160.) I placed some of the tiles in my scene, and then played the scene. The only tiles that were rendered, were the ones covered by the original tileset (the two autotiles.) The tileset editor still showed my changes to the tilset configurations, so I deleted the autotiles, single tile, and atlas tiles, and remade them. This didn't work. I then removed the texture from the tileset and recreated all of the autotile, single tile, and atlas tiles. This also didn't resolve the issue. I closed the project (quit to project list) and then re-opened the project. My tileset now showed only the two original autotiles (as though I hadn't changed them.) Adding my further tileset changes didn't resolve the issue at this point, either. I cleared the tileset resource from the tilemap, and created a new one, with that png file, and created all of my autotiles, etc. This time the issue was resolved.
This happens when the Subtile Size is changed after adding a bitmask.
Most helpful comment
It should just ignore tiles outside the bounds of the tileset tough.
Would have fixed this wierd scaling issue. It is most certainly a bug since scaling shouldn't preserve data which doesn't exist.