Not sure these quality as bugs, per se, but they are issues with the animation.
When Vella is in Shellmound- after she accesses the Dead Eyed God's pyramid and accesses the Beast Hooker perfume
When you go to talk to the Maidens the screen flashes- as if it was going to another shot, but then goes back to the action. It happens every time and is very annoying. EDIT: This happens right before Vella says "Well, see you maidens later."
With Shay-like character in the pyramid/space ship- he never really makes eye contact with Vella, like Vella does with him. It makes him seem less part of the game then she is. Also, after talking with Shay-guy, when Vella is still in the ship but not interacting with him, he is suppose to be fixing his ship. However, he is simply waving his hands around. Possibly this is some way to access the controls, but it is clear that his hands are going over the far side of the controls, not on them at all. This also does not really match up with the controls in the Shay side of the game very well.
Forgive me if this is not something that should be posted here, but they really jumped out at me when I was playing.