The Secret Box / Band Geeks - S2-E14
Audio problem: At the end of "Band Geeks" when everyone is playing "Sweet Victory" at one point Mrs. Puff is shown playing the guitar. When this happens, you can see the others in the background not doing anything, even though their instruments are heard.
Audio problem: When Peter introduces the pope to his friends at work, and he is saying "Remember when we got that stripper for Charlie and it turned out to be his son? I think this is gonna top it" or something along those lines), Peter's mouth very obviously does not sync up with the words being said.
The Honking - S3-E1
Audio problem: After they have welded Bender to the wall Leela and Fry leaves. When they go outside the door is closing. It cuts and we hear the door close but we can see the door is already closed. (00:11:45)
Lust for Royston Vasey - S2-E2
Audio problem: During the Denton's song when they are bringing Benjamin back to the bed, Auntie Val is singing in the hallway but her mouth isn't moving.