Bugs I've found
Some of these bugs may seem a little nitpicking, but I care about the program so much that I want to bring these problems to dev's attention. Also forgive me for my bad explaining skill.
Start a new document and use these settings:
Number of tiles wide = 5
Number of tiles high = 1
Tiles width = 30
Tiles height = 30
Draw something, like a rectangle and use "Tile draw tool" and hold CTRL to assign it as tile. Next create a new layer and use on the second tile the "Tile draw tool" to paint the tile you just created. Then continue doing that until all tiles are filled.
It should look something like this: http://i.imgur.com/LrnuDbk.png
Now choose second layer and select erase tool and start erasing part of it. As you can see it affects all layers.
Note: If you can't reproduce the bug try to manually press the tool icons instead of using a shortcuts and don't make any unnecessary tool changes.
Menus Behave Oddly
When pressing tab in menus it highlights oddest things. For example; when creating a new document and you're choosing what size you want the new canvas to be, it highlights the whole window when you press tab and second press highlights "Tiled document or animation" etc... and then on the SEVENTH tab pressing it highlights the desired "Number of tiles wide" also the content of it isn't selected automatically, means I need to manually erase them.
Also Enter doesn't seem to work most of the time. One example of this is when making a new document. Tab until "Create" is highlighted (btw 'only' 19 Tab clicks) and press enter. It closes the window without creating a document.
Resize Canvas Bug
You can't press minus on your keyboard.
Not a bug but;
Feature: Splash screen should be timed.