Continuity mistake: When Bart hands Ms.Krabbappel his final test, there are some shots going back and forth between their faces. During the first shot looking at Ms.Krabbappel, you can see a window behind her, and outside the window, there is no snow, even though there was a whole lot of it yesterday. During the next shot, the snow IS there. As the camera goes back and forth, the snow disappears and reappears.
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 Homers face, you can see it is now Principal Skinner and Carl standing there.
Plot hole: When Homer is seen at work in the flashbacks (before Maggie was born), he is at his usual control panel in sector 7-G, but he only began working here when Burns made him safety supervisor in season 1, "Homer's Odyssey". Before Maggie was born he should have been working at the conveyor belt with the carbon rods, where we saw him in the first couple of episodes.
Continuity mistake: When Homer sits down in the movie theater, all the rows are completely full, including the row behind him. When he turns around to talk to Selma, the seats directly behind him are empty. Then, when Homer turns back to the screen, the Sea Captain and Dr. Hibbert appear sitting directly behind him.
Continuity mistake: In 'The Genesis Tub,' Lisa sits on a tooth-throne in the tub, which has red cloth draped over the arms with gold tassels around the edge. However when Bart comes to take the tub, Lisa stands up on the throne and yells "Bart, no." - in this shot the tassels are gone.