Continuity mistake: When Homer and Sideshow Bob are chasing the mechanic on stilts, the mechanic tries to get away, and his cape falls off while he is being chased. In the next shot, we see a close-up of the mechanic, and you can see his red cape is back on again. Then in the next shot, we see Homer and Bob chasing him, and his cape is off.
Continuity mistake: After Kirk (Milhouse's dad) drives away from the stadium, Bart and Homer are walking along and you can see the Drink Duff sign right next to the edge of the fence. The next shot of Homer noticing the sign, the sign is further away from the edge of the fence and is smaller.
Other mistake: Bart and Lisa overload the nuclear power plant to create a city-wide blackout so everyone can see the meteor shower. All the lights in Springfield blow out. Yet when we see the Simpsons sitting on their lawn watching the shower, every single window in their house is yellow, as if every room has their lights on. It is the only house shown with power.
Audio problem: In Declan Desmond's film of Springfield Elementary shown at the end, Kearney and Dolph start beating Jimbo up. After Kearney says "Sellout," he says "Yuppie" in Dolph's voice. Then Dolph says "Soccer Mom" but in Kearney's voice.
Continuity mistake: When we first see Willie standing by the Black Wall of field trips, the latest entry is at Willie's eye level. But when the angle changes, there are a lot more names on the wall, making the last entry appear just by Willie's chest.
Deliberate mistake: When Bart and Edna are watching "Holes" in the IMAX theater, Edna sighs and pulls out a locket which we can see the back of. After opening it up to reveal pictures of her and Seymour, we find out its actually a triptych when she opens up another image of Seymour's mother. From the way she unfolds this extra picture, Seymour's mother would have had to be facing outwards, but in the previous shot the back of the locket was blank.