Homer's Barbershop Quartet - S5-E1
Continuity mistake: When you see a shot of the church from outside in the scene where the bee sharps sing there, look closely at the sign. It says 'Also: The Bee Sharps', only they don't name themselves that until later on in that episode.
The Last Temptation of Homer - S5-E9
Continuity mistake: Mr Smithers throws a notepad at the person saying that a real emergency exit is required, but when we see it on the floor it is now a book with a green cover.
Homer's Barbershop Quartet - S5-E1
Continuity mistake: In the flashback where Marge is making a model of Homer, the models head falls off and Santa's Little Helper picks it up, but the Simpsons did not own the dog back then.
Secrets of a Successful Marriage - S5-E22
Continuity mistake: When Homer gets thrown out of the house by Marge and Otto walks up to him, you can see that it is Smithers and Carl standing behind Homer. Yet in the next shot when you see Homer's face, it is now Principal Skinner and Carl standing there.
Burns' Heir - S5-E18
Continuity mistake: When Homer and Marge are talking to Chief Wiggum, the Rubik's Cube and the cup on his desk changes to a doughnut between shots. (00:13:20)
Other mistake: When Homer and Chief Wiggum fall into the waste, in the second shot, the cliff edge looks very weird. It seems to be transparent with Ruth's car floating in mid-air, and there is a big curved wall that doesn't have ground at the top.
Revealing mistake: When everybody is in a big fight at the Do What You Feel Festival, watch out for a man in an orange shirt with black hair. His left eye keeps disappearing for one frame.
Continuity mistake: The man conducting the tour of the box factory tells the children that they will not be able to see a finished box, as the boxes are assembled in a separate location. However, moments earlier we saw a flat box going through a machine, and coming out finished.
Continuity mistake: When the person delivers the animation cell, his skin changes from white, to brown and then back to white. When Bart looks through the letterbox to see who was there, his skin is white. When he gives the box to Bart, it is brown. When he hits Bart in the face and says "that's for keeping me waiting", it is white again.
The Last Temptation of Homer - S5-E9
Continuity mistake: When Homer and Barney are at Moe's, Barney drinks his beer and then his cup his empty, and Homer's is full. Then later, Homer's cup is empty and Barney's cup has magically refilled itself.
Homer's Barbershop Quartet - S5-E1
Audio problem: When the Bee Sharps are singing 'Goodbye my Coney Island Baby' next to the Statue of liberty, you can hear Chief Wiggum's voice singing with the other members of the group, but he got chucked out of the group earlier on in the episode.
Other mistake: In the scene where the Simpsons are viewing the path of the Corvair's Re-entry, the blip representing the spaceship crosses the entire US from North-West to South-East in about three seconds. This is really impossible, even for something going as fast as a spaceship on re-entry would be.
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.
Homer's Barbershop Quartet - S5-E1
Continuity mistake: At the sale, when Bart and Lisa first find 'The Bee Sharps' album, the order of the records in the stack change in subsequent shots.
The Boy Who Knew Too Much - S5-E20
Continuity mistake: Hans Moleman's clothes change from white to black during the trial. (00:12:05 - 00:13:25)
Burns' Heir - S5-E18
Continuity mistake: The doughnut Homer later picks up isn't by the door when Lenny walks into Mr Burns' office, and we never see anyone put it there.
$pringfield (or How I Learned to Stop Worrying and Love Legalized Gambling) - S5-E10
Revealing mistake: At the dinner table Homer says something like "as you know it's always been my lifelong ambition to be a blackjack dealer." During this line, for some reason they appear to have used a clip from an older episode (Season 3 / Episode 3 - When Flanders Failed) and dubbed the line over. For one thing, the animation is of a much lower standard than the rest of the episode. And perhaps even more telling, when he says it, he is holding a fork with some food on it, but from the earlier shots we know there is no food in front of him.
Continuity mistake: When we first see the power sander, there is only a white patch on the side. In the next shot when we return to viewing it, "Property of Ned Flanders" has appeared.
$pringfield (or How I Learned to Stop Worrying and Love Legalized Gambling) - S5-E10
Continuity mistake: When Marge comes home after the bogeyman incident, Homer trips over a footrest. You can see Bart sitting there however his pyjama's are a dark green color when before they were a bright green color. (00:16:35)
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