Plot hole: The Toymaker throws that toy bird at the hippie version of himself. The toy goes through him because he is a hologram. Later, he pushes the soldier version of himself at the screen making it crack. How could he if the three others are holograms?
Factual error: Dinky Winks has a branding iron that says 'Dinky' when it faces out, but we should be reading it backwards. When he uses this brand, then it will be backwards.
Continuity mistake: In the scene where Juni finds Carmen in Level 4, they are on a cliff. They begin crossing a virtual bridge, then in the next shot, they are back on the cliff.
Continuity mistake: When Juni protests that he can't beat Arnold in Level 3, Juni has a silver plate on his life count. It wasn't there before the battle, and after that shot it disappears.
Deliberate mistake: After the game has entered the real world, and Floop and Minion are there to "save the day", Carmen and Juni throws seven pairs of glasses to them. But afterwords, we see there are only four pairs of glasses on Minion and one pair on Floop, which totals five.
Other mistake: If "Little Dink" isn't wearing 3-D glasses, how does he know what's going on when he tosses the branding iron to his dad?
Continuity mistake: When Grandpa picks up 2 of the programmers and makes them appear as they really are,in the next shot,the 2 he picked up are standing behind juni,and 2 different kids are in his arms.
Plot hole: Doesn't it seem a little strange that Arnold, Francis and Rez are still in the game with Juni even though they started before him? We find out they were sent back to the beginning due to Francis cheating in the Megarace. Juni wasn't required to start again and he gets to Level 5 with only 5 minutes left . So shouldn't their time have long since run out?
Continuity mistake: At the end of the movie when you see everyone put their hands in & say, "To Family", the Toymaker says, "Aaaaaand, BREAK.". If you pause it when R.A.L.P.H is hurdled into the air, you can see that half the people are gone.
Continuity mistake: When the programmers are teasing Juni, you see Grandpa in the mist. When Grandpa picks the programmers, you can see the camera move slightly. In other words, you can see that it is 2 different shots.
Character mistake: Before the Megarace, Rez looks back at the camera and says that they'll try to help him out-but you can see Juni's tires in front of Rez's car. In a shot before this one, Rez says Arnold will crush Juni-looking at the camera, which is in front of Rez.
Continuity mistake: When Juni lifts the fishbowl with the miniaturized sharks in it and says "Ralph, write a thank you note to Romero" the bug picks up the pencil and draws a line on the pad of paper, the spider monkey then interrupts him and the bug and the spider monkey are fighting with their implements, they show the pad in the foreground of the fight and the line has now disappeared from the paper.
Other mistake: When Juni and Carmen are fighting the robots and Dad flies down, Carmen has an armful of glasses. How did she know she would need that many glasses. She didn't...at least she didn't leave the building with them..
Continuity mistake: Through out the Megarace the purple vehicle changes from a tall one wheeled bikey thing to a large four wheeled vehicle.
Other mistake: Near the end when Juni and the gang are fighting those robots. It is clear daylight, but isn't it weird that there are NO people in the streets? A place like that should be crowded with people, or at least a few.
Factual error: Francis is actually wrong about the lava/magma in Metroid. There is quite a bit of lava above the surface in a few Metroid games.
Continuity mistake: During the scenes in the real world after they have come out of the game, Juni and Carmen give glasses to their dad who is in front of them, but in the next scene he runs at the giant robot and Juni and Carmen are nowhere to be seen. This happens a lot with other characters throughout this section of the movie.