Continuity mistake: Milhouse is seen in the school bus during the Lisa segment, even though he was with Bart at the time.
Audio problem: When Homer and Marge are driving to the hospital, Marge says "Let's just say that Bart did it". But her mouth says something else when she says "Bart".
Continuity mistake: The bikes disappear after Bart and Milhouse arrive at the cave.
Continuity mistake: During Lisa's and Bart's segment, time seems to run really quickly. When Lisa leaves West Springfield Elementary it is 11:00 and when she gets to Moe's it is noon, then a few minutes later it is 2:50. When Bart and Milhouse find Fat Tony it is noon, then when Bart gets hit by the truck, it is almost 3:00.
Audio problem: When Bart is going through his keys, he says "Your house", and his mouth doesn't match what he is saying.
Audio problem: When Marge says "We've gotta get to the hospital, Homer" her mouth doesn't move.
Audio problem: When Lisa says "Oh no, somebody took my bike", she is mouthing something else.
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