I followed the guide about this problem. This is actually the guide I followed when my SOR Blaze character glitched. But I decided to remove the hacks from the trainer and pokemon, but the problem still remains. I first thought it was a code I didn't put in, but it wasn't that. So it's something else, I just don't know what that something else is.
Edit: I figured it out, it was related to the codes I entered. I just wish it wasn't the stage expansion codes.