Continuity mistake: Game Over: When the manual is shown falling down to Springfield, the alley way that Bart is shown walking down appears to be one straight path. When this same alley way appeared earlier in Bartman Begins, Bart was shown turning around a corner that doesn't appear to be present in the overview shot. The corner can be seen when the shot of the manual landing on the ground from Bartman Begins is replayed.
Other mistake: Game Over: In the flashback of God losing the Simpsons Game manual whilst playing the game, when the flashback starts, he is shown pressing the buttons as if he were playing, and then takes out the manual because he has difficulty with the camera settings. But on the TV, we can see that the intro cutscene for Bartman Begins is playing, so he shouldn't have been using the controller at all for that part of the game.
Continuity mistake: Game Over: When God says to the Simpsons that the Simpsons Game was a mini-game inside his Earth game, Bart is shown standing slightly ahead of Lisa, and Marge is standing slightly ahead of Homer. When the shot cuts to a closer angle of them, Bart and Lisa are side by side and Marge and Homer are side by side.
Continuity mistake: Game Over: When God is telling the Simpsons about the Planet Earth game, the Simpsons are standing side by side. When the shot cuts to an angle higher up, Bart and Lisa are suddenly in front of Homer and Marge.
Continuity mistake: Game Over: When God is explaining to the Simpsons who they really are, all the Simpsons are standing next to each other, side by side. Then it cuts to a shot of Bart and Lisa, where Bart says "We knew that, Birkenstocks", but they are the only ones in frame. From this angle, at the very least, Marge should have been seen next to them.
Other mistake: Game Over: When everyone reaches heaven after climbing the stairway, there are a few other characters with them, such as Barney, Private Burns and two Game Engine workers. These characters are never heard from again for the rest of the level. They are not present in any of the gameplay, the cutscenes or even the rest of the opening cutscene after the gate closes, despite having the same goals as the Simpsons.
Other mistake: Game Over: Once Lisa has finished building the stairway to heaven out of Springfield buildings, the main characters and a crowd of at least twenty people are shown beginning to run up the stairway. Once they reach heaven, there are only about four other characters shown running through the heaven gates alongside the Simpsons.
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.
Continuity mistake: Game Over: When Marge says all they can do is pray that God saves us, Lisa (who is standing in front of Marge, but turned away), turns her body around 90°, and then turns her head to the right 90° so she is looking at Marge. When the shot cuts to Lisa, she is facing Marge directly.
Character mistake: Game Over: After returning from the Game Engine and Bart points out they are still under attack, Marge says "I guess all that's left to do is pray that God saves us." When she says this, Lisa can be seen smiling, but the town is still under alien invasion so there should be no reason to do so. She doesn't come up with the idea to use her Buddha Hand powers to talk to God until right after Marge says the line, so it couldn't have had anything to do with that.
Other mistake: Game Over: Once everyone returns from the Game Engine, Homer sits down on the couch. The house then rumbles, prompting Bart to walk over to the window and say "Homer, we're still under attack." When Bart says this, he looks over to the left side of the living room. But the window is in the centre of the room and the couch directly faces the window, so there is no way Bart could've been looking at the couch to say the line to Homer.
Continuity mistake: Game Over: When Bart points to the doors to get back to Springfield, we can see that there is a red carpet leading up to the doors. In the next shot, the red carpet is much narrower.
Continuity mistake: Game Over: When everyone is escaping the Game Engine, Mr Sparkle can be seen exiting the Big Super Happy Fun Game level. In one shot, he is a couple feet off the ground. But in the next shot, he is several meters in the air.
Other mistake: Game Over: Whilst the Game Engine is collapsing, there is a shot of the video game characters escaping their respective games, shown from on the ground, while the Simpsons toward the door back to Springfield. To the right, a character can be seen exiting the Big Super Happy Fun Game level, but the door behind him is closed.
Revealing mistake: Bartman Begins: When Bart is walking through the alleyway, complaining he only has the games he bought yesterday, he steps on top of a discarded wrapper, but wrapper is unaffected by getting stepped on by Bart's foot. It remains in the same position and is never shown bending.
Revealing mistake: Mob Rules: When Lisa is asking Marge if she finds it hypocritical that she is opposed violence in games, yet she used violence to get her way, the body movements used for the mob appear to be repeated and reused throughout the shot. Every time they are shown waving their arms, they appear to move in the exact same way.
Other mistake: Mob Rules: When Quimby, the game producer and the two interns get out of the hot tub, no water can be seen dripping off their bodies and onto the floor.
Character mistake: Mob Rules: Marge is reading a newspaper regarding senators trying to push Mayor Quimby to ban Grand Theft Scratchy. She looks at the bottom of the page and discovers Quimby is cosying up to a sleazy video game producer; she disapproves of this, but she appears to be smiling when saying "That really burns my beehive" despite there being no reason for her to do so.
Revealing mistake: Invasion of the Yokel Snatchers: An alien takes the coupons that Cletus is holding. After looking at them, the alien throws each of the coupons to the ground, one by one. The same animation is reused for each of the coupons falling, as shown by the fact that all of them appear to fall to the ground in the exact same fashion.
Factual error: Lisa the Tree Hugger: After saving Lenny and Carl, Bart aims his slingshot at the target controlling the factory and fires a stone from the slingshot, hitting the target. Once the stone hits the target, debris from the impact can be seen flying off the target showing that it has been destroyed, but as the dust clears, the target is virtually intact.