Continuity mistake: Enter the Cheatrix: When Lisa knocks on Professor Frink's door, the box of band candy that Bart is holding has no text on the right side of it. Bart then raises the box saying "I gotta move this candy" and the words BAND CANDY have suddenly appeared on the side of it.
Continuity mistake: Enter the Cheatrix: When Bart and Lisa approach Professor Frink's front door, in the wide shot, Bart and Lisa step on the front step and Bart is shown standing on the left hand side of the step and Lisa is standing on the right hand side. When the shot cuts to a closer angle of the two, Lisa is standing more to the middle.
Other mistake: Lisa the Tree Hugger: When the factory explodes, Lisa is standing outside the entrance looking at a damaged sign break off the wall. Everything that Bart and Lisa did to destroy the factory occurred within the confines of the company, so there is no reason that the sign should be tattered or broken off.
Continuity mistake: Lisa the Tree Hugger: When the cutscene opens on Bart and Lisa standing outside the logging company, the establishing shot shows them with their backs to the main door. When the shot cuts, they have rotated 90° so that the main door is positioned to their left.
Continuity mistake: Game Over: In Bargain Bin, when the mothership fires on the Simpson house, it destroys the mailbox. When they return in Game Over, in the establishing shot of the house, the mailbox is suddenly back and intact.
Revealing mistake: Mob Rules: When Marge and Lisa witness Martin carjacking Ned, in the shot of Martin saying "Gimme your ride, jerk", Marge raises her hand to her mouth. When she raises her hand, part of the baby carrier she is carrying Maggie around in is not fully drawn in.
Other mistake: Mob Rules: In the opening cutscene for Bartman Begins, Uter, Ralph, Jimbo, Dolph and Kearney are seen queueing outside the Sequel Stop store. In the opening cutscene for Mob Rules, the exact same group of people can be seen coincidentally queueing outside the same store, despite the passage of time.
Revealing mistake: Bargain Bin: When the Simpsons are sitting at the computer, the Ethernet cable seen coming out of the back of the computer doesn't appear to lead anywhere. The Ethernet cable is shown attached to the computer, but it ends after a few inches and is not attached to anything else. The animation for the cable was incomplete.
Continuity mistake: Big Super Happy Fun Game: When Homer is handed the Sparklemon after he and Lisa defeat Ralph, his left arm is raised when he grabs onto it. In the next shot, his left arm is at his side and the Sparklemon has disappeared. The same mistake is also made when they defeat Sherri and Terri.
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.
Character mistake: Bargain Bin: When Bart is researching the Simpsons Game online, he says "Bartman, eating contest, alien invasion, slaughtering dolphins, it's describing everything we've done all day." Even if we were to assume the events of Bartman Begins through Mob Rules took place over one day (which is already hard to believe), the family were shown sitting at the breakfast table in the morning during the Mob Rules end cutscene, so there is no way the entire game took place over the course of one day.
Character mistake: Invasion of the Yokel Snatchers: When Homer and Bart witness Cletus getting abducted, Bart tells Homer "they're torturing that yokel", almost as if Bart doesn't know who he is. The Simpson family has interacted enough times with him throughout the series to know who he is and that his name is Cletus.
Continuity mistake: Mob Rules: When the mob begin cheering after Quimby bans Grand Theft Scratchy, they are standing on the curb. When the shot cuts, the mob is now standing on the road and Marge and Lisa are the only ones standing on the curb.
Continuity mistake: Mob Rules: When the Scratchy statue is knocked down, the head rolls away and crashes into Town Hall causing part of the building to collapse. Two window frames can be seen falling beneath the rubble. When the shot cuts, the window frames are suddenly above the rubble.
Revealing mistake: Mob Rules: After part of Town Hall collapses, the shot cuts to Marge and Lisa. Lisa can be seen holding a lit torch, but for the first frame of the shot, the fire doesn't appear to have been animated onto the torch. The fire just pops up on-screen a few frames after the shot starts.
Continuity mistake: Bargain Bin: When the mothership flies away from the Simpson house, the family are shown standing next to a small wall. In the next shot, they are standing a few meters ahead of it.
Continuity mistake: Bargain Bin: When the family are in the living room looking at the Video Game FAQs, a drawer can be seen on both sides of the couch. Both of these drawers have a shelf below it, with three books shown each of the small shelves. A couple seconds later, when the Simpsons get transported to the Game Engine, the books have disappeared from the shelf closest to the window.
Other mistake: Big Super Happy Fun Game: When the three Sparklemon confront Milhouse, they begin beating him up, but it is very clear their fists are not touching his body.
Continuity mistake: Big Super Happy Fun Fun Game: When Milhouse loses his powers and hands Homer and Lisa the keycard, the amount of rocks on the ground change between shots. At first, there are two rocks behind him to his left, but when the shot cuts, there is only one rock behind him to his right.
