There have been quite a few topics regarding oddities nad possible glitches in the game. For the sake of convenience I'm compiling them all into one list. If you've found something not listen here, let me know and I'll add it.
The List:
- Baretta talks when you find the Final Eye, even if you didn't re recruit her.
- The Elemental orb quest seems to not display the number found correctly sometimes. Not sure about this one.
- Save bunny in the Catacombs disappearing when starting a new file? Dunno about this either...
- Sparks sometimes picks up a Chimera Egg from an enemy in the Rillian Colosseum, but it does not show up in inventory.
That's all I can recall people mentioning right now, Though I think there are more.