Continuity mistake: Just after Homer has used the proton accelerator, Dean talks to him. In this scene he is writing something on a piece of paper, but he writes on the same line every time. He finishes writing on that line, then starts on it again.
Audio problem: When Homer is talking to the family about their complaints about the nerds, he says something that ends in "where we can all live in harmony". When he says this the audio does not match his mouth movements.
Continuity mistake: The colour of the alien poster in the nerds' room changes from pink to blue.
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