If you select and copy a certain amount of pixels in the editor, and then try and paste it into a smaller icon's frame, it can change just that frame's dimensions. I ended up with a 32x40 tile in a 32x32 icon, for example (the issue isn't apparent until you go back to the list of frames, and then re-enter the editor, at which point the canvas will change sizes).

EDIT: Steps to reproduce:

1) Create two icons, one with the dimensions 32x32 and one with the dimensions 32x40 (that was the size I personally needed, so I can confirm it happening with that size).

2) Create an icon of some sort in the 32x40 icon. Doesn't really matter at all, blank pixels might even work (I used a movie, but that probably isn't necessary).

3) Create a movie in the 32x32 icon.

4) Copy the 32x40 icon into a frame of the 32x32 icon. The canvas size of that frame should change.

That should reproduce it. However, I hit the paste button a couple times and crashed DM, so I'm going to look into that now.