Hey, can you tell us where it happened? It could be a wrong jump in the code.
Sorry it was quite a few days ago so I can't remember the exact scenes but I can tell you what I did. I didn't really encounter any glitches pre-exile. Once leaving the town, I focused on doing as many side-quests (character-specific stuff) as I could before the main story. If you start a new save and do this, you'll probably encounter it too. (all of the glitched scenes I mentioned come from the character-specific stuff) Though it could be possible I may have updated the game wrong at some point (idk)
EDIT: I know the late Cleos stuff with the little girl happened for me before the red suit first appeared in the main story. And I could do the later Estia stuff before the guild lady moves into our home. (Sorry I'm bad with names) These are only a few examples I could remember.