I've got two bugs both present on the using Banjo Tooie (U) rom.
There appears to be a slight sound glitch, possibly related to the game's timing. If you watch the demo reel at the start (viewable simply but running the game and not hitting anything) and reach the fourth demo it becomes apparent at the start. It's also noticeable in the 6th. There was a similar problem in earlier versions of Bizhawk with the "King Jingaling Gets Zapped" cutscene however that problem has since been corrected, so it could be something similar. I'm aware this is something miniscule but thought I'd bring it up anyway. It's present in any resolution and in both playback and video dumps, so it shouldn't be hard to re-create the problem.
Also when dumping video I'll occasionally get this error:
It's happened in pretty much every N64 title at one point or another but the frequency varies. I think it's happened once in Banjo Kazooie, whereas it happens frustratingly frequently in Tooie. These are just example games, it's present in others too.
Bizhawk's fantastic overall though!