Tree House of Horror V - S6-E6
Continuity mistake: When Skinner is cooking the kids, he and the cook are chasing Bart, Lisa, and Milhouse. From the back, he has an apron tied around his neck. In the next shot, he puts on an apron.
Continuity mistake: When Bart is first introduced to the Superfriends, Ham moves around the table a bit. First he is seen sitting next to the kid with dark, curly hair, and you can see a plate in between him and Bart's plate, indicating that someone else is sitting there. This someone turns out to be Lisa, who after she is introduced, switches seats with Ham, making Ham sit next to Bart.
Homer vs. Patty and Selma - S6-E17
Continuity mistake: When Homer is walking upstairs after kicking Patty and Selma out for the second time, the wall that Homer was approaching is a darker colour than it usually is, and Homer walked up the stairs slowly. But a second later he closed a door, indicating that he went into a room. Are we really to believe that he could go very quickly from the stairs to a room in a matter of seconds?
Continuity mistake: Before Bart notices the lemon behind the lemon-shaped rock there is actually no lemon there. We can later see that there is too much of a significant gap between these two objects for the lemon to be hiding behind the rock.
Continuity mistake: Just before Homer (dressed as Krusty) is picked up by Officer Wiggum, his car is brightly painted and has wobbly clown wheels. When he pulls over it's back to the ordinary dented purple car he usually drives.
Homer Badman - S6-E9
Continuity mistake: Just after Marge's left jacket pocket bursts open at the candy convention the shot changes to a shot of Marge's face. The next shot her right pocket has suddenly burst as well and the candy in it is no where to be seen.
Grandpa vs. Sexual Inadequacy - S6-E10
Continuity mistake: While hiding the fact they are looking at sex books from Bart and Lisa, Homer picks a green book. When we see what he's reading, it's a grey "Maple Thorpe" book.
Homer Badman - S6-E9
Continuity mistake: When one of the pockets of Marge's coat explodes (when Homer is stealing the rare Gummi), a huge pile of candy comes pouring out. When she bends down to pick some up, there isn't nearly as much candy there as before. There are people picking up the candy with her, but they would have to pick it up extremely fast, and they aren't.
Tree House of Horror V - S6-E6
Continuity mistake: When the Simpsons shed their skin at the end, the skin falls to the floor. In the next shot it's gone.
Tree House of Horror V - S6-E6
Continuity mistake: In the third story, the five remaining students are all in one classroom - Bart, Lisa, Milhouse, Wendell, and Ralph. Ralph disappears when the other four try to escape.
Continuity mistake: As Homer is giving his speech to the dressed up monkeys, all of the monkeys are dressed in blue suits and you can also see there is one monkey next to the stairs on the stage. In the next shot of Homer leaving the stage there is now six monkeys, with only one wearing a suit and it is grey. (00:19:45)
Who Shot Mr. Burns? (1) - S6-E25
Continuity mistake: Principal Skinner picks up the hamster and throws it away. But his hands are clean as a whistle even though all the hamster was covered with oil.
Springfield Connection - S6-E23
Continuity mistake: When Hans Moleman and Rev. Lovejoy are in the prison they are sitting to the far right of the bench (which is nearest to Homer's cell). Then in the next shot they are to the far left.
Springfield Connection - S6-E23
Continuity mistake: In the police station the blue light on the ceiling disappears from when the police are seen laughing at Marge.
Continuity mistake: When wedding has been just called off, Lunch Lady Doris calls everyone for wedding cake, and among people who rush to it we can see Moe (you can recognize him by his eyepatch), then, Lisa starts to walk off and among the people she passes by you can see both Lunch Lady Doris and Moe.
Continuity mistake: When Homer is kicked out of Moe's the window behind Homer suddenly opens so Moe can throw the record out.
Who Shot Mr. Burns? (1) - S6-E25
Continuity mistake: In this episode, Mr Burns and Smithers are on the balcony of Burns' office. Mr Burns says "It will be like taking candy from a baby. Hey, that sounds like a laugh. Let's try it right now." We see Smithers, whose expression doesn't change as the two go back into Burn's office. In 'Who Shot Mr Burns Part 2', Smithers remembers this event, except now he looks quite shocked when Burns mentions about taking the candy.
Springfield Connection - S6-E23
Continuity mistake: When Marge walks into the hair salon, she is carrying a white bag. But in the next shot when she talks to Mrs Krabappel, the bag is gone.
Who Shot Mr. Burns? (1) - S6-E25
Continuity mistake: During The Town meeting scene, the position of Latin jazz great Tito Puente hops all over the room - he is frequently appearing in the background, but from various angles.
Springfield Connection - S6-E23
Continuity mistake: When Marge sees Homer's car parked illegally over 3 handicapped spots you can see a car parked near Homer's that is orange. Later in the scene when Marge starts writing a ticket up for Homer the car next to Homer's is now a dark brown. (00:14:35 - 00:15:05)
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