I have not been. The only part of tilesets I've ever touched is creating my own (distortion world) and adding an autotile of lava to the default cave and outside ones.
I can think of two reasons this could be occuring, as these are really the two similarities between Melanite and this one.
It could be becasue we are using .gifs for the battlers, though I find this unlikely. It is far more probably that the glitch is caused by the pokemon following the player, somehow. Perhaps there is a bug while loading the follower.
Is it safe to have the tilesets refresh after every battle (which is when they seem to happen)? Or would that cause more problems then it solves?
I've never heard of this bug before. Certainly it's never happened to me.
The tileset graphic is loaded in the def initialize of class Spriteset_Map, and is saved within an instance of class TilemapLoader (which also does the rendering of maps).
I have no idea what could cause this to happen, unless you've been making some uninformed changes to certain parts of the code. The odd part is that just the tileset appears to have been disposed or set to nil, leaving the autotiles alone.
Have you been trying to do anything fancy that would affect the tilesets at all? For example, using different tilesets based on season?