Before the cast begins singing "Good Ship Misery", the dubbing for the coupled penguins in the cage is swapped during the line "Welcome Hubie! Although Welcome probably isn't the appropriate word."
During the musical number "Good Ship Misery" there are a few shots where the entire chorus is sliding back and forth on a raft of sorts, and there are several seconds of the background singers being completely inanimate, simply sitting there frozen in place.
Towards the end as Hubie and Marina kiss, Rocko and several applauding penguins surrounding the pair stand frozen and glitch three times, and Rocko's mouth never closes.
In the beginning when Hubie is singing "Sometimes I Wonder", there are several instances in which the animators did not complete drawing Hubie from the waist down. This is clearly visible in several shots in the bottom of the frame.
During the opening credits, when you hear a man and woman singing about pebbles, there is a mismatch between the sheet music on screen and what is actually sung. The woman's line indicates that the notes should go down as she sings "forever," but her voice goes up instead.