The route 3 glitch sometimes happens at the beginning of route 3 after fighting the first tamer. You lose control of the player and gain control of an npc who has a very restrictive walking area, and the only way to "fix" it is to load your save. Of course the glitch will just occur again so it isn't really fixed
I have no idea where to start, but I've only been able to recreate the glitch once so maybe it isn't game breaking. On all my other games I managed to reach mt. Moon with no problem, so it isn't too common of a glitch.
Anyway, it's proving to be a very difficult thing to fix but I'm still trying.