Oh, I just attributed everything else to the save breaking. Nothing else is broken apart from what I mentioned, it just doesn't fix itself when I restart the game without saving. I will also probably try recreating this because I started after I completed the game and I think I can get them to turn almost every tile into a mossy brick. I'm guessing it had something to do with there being too many mites in the the game when I saved, but that's just a guess.