Deliberate mistake: Game Over: Just after the gates to heaven have closed on Homer and Bart, the two look up and see Shakespeare standing on a floating cloud just above the gate. However, in the initial wide shot of the gates when everyone else was running through it, Shakespeare could not be seen floating above it, presumably to make his character reveal more amusing.
Deliberate mistake: Bargain Bin: When Homer mistakes the video game boss for his literal boss, he takes out a clipboard so that he can look busy. Aside from being part of the set up for a joke, there is no reason for Homer to have this clipboard on him, nor would there have been anywhere for him to have been hiding it (unless it was just tucked into the back of the trousers).
Deliberate mistake: Game Over: When God has finished explaining how the Simpsons Game manual ended up landing in front of Bart, Homer raises a baseball bat with wings on. While it makes for an amusing moment, this bat was never seen in Homer's hands at any other point in the cutscene, nor was there anywhere for him to put it.
Deliberate mistake: Game Over: When the large crowd of people are looking at the complete stairway to heaven, they are standing a large distance away from it. Then suddenly, the crowd is right in front of it. The crowd and the stairway are not shown in the same shot, but Lisa (who is standing in front of it) looks to the crowd and says "Come on everyone" and they proceed to run up along with her, so they are closer.
Deliberate mistake: Five Characters In Search Of An Author: Various times throughout this level, Matt Groening draws on some paper and some cartoons come to life. Whenever this happens, he only draws on one piece of paper, yet several pieces of are shown with cartoons on them.
Deliberate mistake: Grand Theft Scratchy: If Lisa strikes her lightning hand on a member of the mob, that mob member won't get injured at all.
Deliberate mistake: Enter The Cheatrix: Any time in this level that shows one player jump into a pipe, the next scene shows two players exiting the pipe at the same time.
Deliberate mistake: Invasion of the Yokel Snatchers: When Kang is arguing with Kodos about not picking up his space rake, there is nothing on the floor around them. Kang walks forward a few feet and suddenly a rake suddenly appears on the floor.