Deliberate mistake: When Homer pushes the trampoline off the cliff, there is no rock below the falling trampoline. However, in the shot at the bottom a tall rock is visible which was drawn there on purpose for the trampoline to bounce off of, despite not being visible in the first shot.
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.
Factual error: In "Nightmare On Evergreen Terrace", Martin has a dream, in which he speaks Latin. At one point, he says a verb that doesn't exist: "morire". The words is "mori" (to die), "moritur" (noun dies) or "moreris" (you die). The "moirie" is also on the blackboard behind Martin.
Continuity mistake: In "Krusty Gets Busted", Krusty's natural skin colour is established as yellow. In "Brush With Greatness" we see him wiping off the clown makeup to reveal that he has yellow skin. But in "Homer's Triple Bypass", he comes to visit Homer, with his white clown face, and tells him that "this isn't make-up". Other episodes after that also show that his skin is white.