Marge vs. the Monorail - S4-E12
Plot hole: When Homer is trying to stop the Monorail, he grabs the big M from the side of the train and uses it as an anchor. However, when the M cuts through 'Springfield's Oldest Tree', there is no visible monorail track or supporting pole in the background.
Plot hole: When Bart prank-calls Moe and tells him his name is Jimbo Jones, Bart says that he lives at 1094 Evergreen Terrace instead of 742 Evergreen Terrace, where Jimbo and Bart are. If Moe had taken those directions, he wouldn't have arrived at the house, instead he would have gone somewhere different. (00:18:30)
Tree House of Horror III: The Simpson's Halloween Special III - S4-E5
Plot hole: At the theatre in the "King Homer" bit, the audience are treated to a traditional showgirl spectacle. But the girls have no curtain behind them, and so the audience should have seen Homer the ape, but they act completely surprised a minute later when Homer comes on. (00:11:40)
