Brother's Little Helper - S11-E2
Audio problem: Homer's mouth is out of sync when he's naming celebrities who use drugs.
Tree House of Horror X - S11-E4
Audio problem: In "Desperately Xeeking Xena", Xena is put in a plastic pouch. Wouldn't her voice sound muffled?
It's a Mad, Mad, Mad, Mad Marge - S11-E21
Audio problem: When Becky is walking towards Otto in the wedding, there is a band playing music. You can hear singing but the singer's mouth isn't even moving.
Answer: I'm not sure if this is the one you're thinking of, but an episode of "Ray Bradbury Theatre," called "A Sound of Thunder," dealt with a similar matter: a group of hunters travel back in time to hunt dinosaurs, only to find things have changed when they get back because someone stepped on a butterfly.
Xofer