Our Vines Have Tender Apes - S3-E20
Audio problem: Towards the end of the episode, the castaways read Tongo's note that he can't take them back with him due to how he behaved with the gorilla. Mr. Howell yells "we won't tell anyone!" followed by other random comments from the others for Tongo to come back. Tongo leaves and as the camera pulls away from the castaways, the same audio repeats itself even though this time doesn't match what anyone is saying.
Pass the Vegetables, Please - S3-E3
Audio problem: As Gilligan gets up to lift the stool he was sitting on, we hear the sound of wood scraping on the floor, but it's on sand.
Answer: Bob Denver answered this when he was on a talk show hosted by Pat Sajak. He said they were going to write into an episode where the castaways found all these clothes, but it got too complicated, so he said, they decided, "who cares, it's only a TV show," and forgot about it. So the writers and actors even asked this, they just never bothered to address it.