Other mistake: When Nelson puts the intestine into the model's mouth, the size of the gut should not increase. It is the same amount of stuff going in a cycle, so where does all the stuff come from? (00:03:15)
Other mistake: The amount of gunk that come from Bart's model at the start is not proportionate to the size of the model. In other words, there couldn't be enough gunk to cover the entire inside of the bus.
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