Okay, this one is starting to really get on my nerves, but:
Whenever I rearrange tiles that are used for item sprites and weapons/misc sprites, it ruins my weapons/misc sprites in 2 different ways:
1. The weapons/misc sprites whose tiles I move are still defined to their old location instead of their new location.
2. It changes some of my other weapons/misc sprites, even though I didn't even move their currently selected tiles in the tile set.