Plot hole: Game Over: When the Simpsons return from the Game Engine, Springfield is still in the middle of an alien invasion. Lisa then comes up with a plan to build a stairway to heaven out of Springfield buildings, but she is able to build the stairway without the aliens interfering in any way. In fact, there appears to be no sign of the aliens at all, despite the fact that they are currently in the middle of invading the town.
Plot hole: Five Characters In Search Of An Author: The opening cutscene ends with all five members of the family entering the gates to Matt Groening's mansion and walking down the path. Another cutscene then begins to play that continues on immediately after the previous cutscene where Homer and Bart are outside the mansion, but Marge, Lisa and Maggie are nowhere in sight. Since this cutscene continued on right where the previous one left off, there's no way they could have split up so quickly.
Plot hole: Bartman Begins: When Jimbo reveals to Bart that Skinner hired them to rob the museum, Bart says "Principal Skinner?" and looks to his right and sees Principal Skinner standing there. The problem in this scenario is that there is nothing there to make Bart look towards the right. Skinner was never heard approaching nor did he ever state he was there before Bart looked and no-one else in the scene even told Bart that Skinner was approaching.
Plot hole: Bartman Begins: Whilst Homer and Bart are in the museum, they discover that the school bullies Jimbo, Kearney and Dolph are in the middle of robbing the museum. However, in the opening cutscene for this level, they were also seen standing outside the video game store just mere minutes earlier.
Plot hole: Whilst you are in the Game Engine, Homer may say at one point, "Turtle bride, why didn't I think about that?" This is a clear reference to Professor Frink's turtle bride we met earlier in Enter The Cheatrix. The main problem with this quote is that Homer didn't even know about Professor Frink's turtle bride. It was only Bart and Lisa who even knew about the turtle bride as they rescued Frink and only them who rescued Frink in Enter The Cheatrix and met the turtle bride soon after. And although, Frink was in that large box in the theatre, the only thing he ever did was to give Homer and Lisa a power upgrade. Plus, the turtle bride was never visible in the theatre and Bart and Lisa never mentioned this to him.
Plot hole: NeverQuest: A cut scene plays straight after Homer finally defeats The Dragon at the very end of the level. This cut scene shows Homer retrieving the key card for this level from The Dragon's nest. There was no way for Homer to know the key card was going to be in The Dragon's nest. Especially since the walls of the nest were significantly taller than Homer was, which would have completely blocked all view of the key card.
Plot hole: Bargain Bin: After Homer and Bart save the 8-bit Simpsons from being burned in the furnace, Homer and Bart run into an elevator while the 8-bit Simpsons remain inside the "Escape from Krusty Island" game. When the elevator opens, the Simpsons walk into a theatre and discover the 8-bit Simpsons are there waiting for them. How did they get there so quickly? There certainly would be no time for them to escape the game and get to the theatre before the Simpsons did as the Simpsons had a huge head start on them.
Plot hole: Enter The Cheatrix: The level shows Bart and Lisa chase the ape holding Professor Frink. Each part of the level consists of Bart and Lisa running through each place the ape went through. If that is so, while it has been shown to jump a few meters, it doesn't make sense how the ape was able to jump over two huge buckets of blood that was almost five times as more as a jump than it can usually handle. Even if the ape swam through the blood, there should still be blood on it or Professor Frink's clothes.
Plot hole: Principal Skinner got arrested in "Bartman Begins" for getting the bullies to steal from the museum. Yet in "Mob Rules" (which takes place on that same day), he is seen outside Springfield Town Hall instead of being in jail. Marge did break Snake out of jail earlier in the level, but Skinner was never seen in jail.
