Oh wait, i know what you are saying, i remember when i was inserting the second gym tiles, when i was block editing, i placed the tiles over some blank spots, and on the first gym map, some tiles were messed up, it's sorta confusing, because if you try to block edit on the blank spots, (like brownish spots) they change the tiles of the other indoor map, but that's only for tileset 2,i've also noticed that in the first tileset, when you open up different maps, the tiles you insert appear in different colors, which is sorta weird.
so there is no story planned out? What exactly did you want to do? (i'm curious)
Well i think only animated ones would do something like that, and since i never tile inserted indoors for r/s/e, it might be different,I'll make sure to have a backup before inserting them then.
So what about you, how's your secret project coming along, although it's not so secret because you have it in your sig :P