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.
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. (00:08:20)
Plot hole: Dr Marvin Monroe says to Marge he was gone for a long time because he was sick. That's impossible because he died in a previous episode and you can even see his tomb in the episode where Maud Flanders dies. [It could be argued that Monroe really was sick. It was never explained how he died and no one mentioned that he really was dead. The grave, the hospital named after him were in the simpsons universe with the belief he was dead. The clip show mentioned his death but alluded any specifics. As Marge mentions she thought he was dead and so could everyone else on the show.]
Other mistake: When the wheel falls off Bart's skateboard, in the shot where he curves left sharply, you don't see the school in the background. How could he be at the social club if he just left school? (00:05:20)