Visible crew/equipment: At the beginning when Chuckie is turning on all the toys in the office, he flies a helicopter and the string is so visible its funny. The helicopter then crashes and you can still see it. In the next shot the man looks at it and there is no string. (00:11:15)
Continuity mistake: When Chucky and Andy are fighting in Andy's room Chucky has a pocket knife. When Andy kicks Chucky he drops the knife and it goes under the bed. Then if you look closely when the guy walks into the room you can see that the knife moved from under the bed to beside the chest in his room. (00:37:25)
Continuity mistake: When Chucky is thrown down the skull mountain in the horror house, he falls face down towards the fan. But when he lands in it, he's not only face up, but the amount of damage to his face that he received earlier on has changed as well. (01:21:05)
Factual error: When the school starts the war games and Chucky switches the paint rounds for live ammo and a few people get shot, this is impossible because those types of guns have been modified so they can't fire live rounds. All Chucky would have done is taken away their ability to fire anything.
Continuity mistake: When Tyler is going upstairs with the package that has Chucky inside, he collides with a boy up the top of the stairs (the boy was going down) and the package is knocked from Tyler's hands and falls down the stairs. In the shots of the package rolling down the stairs, the boy with whom Tyler collided should also be seen going down the stairs. Instead he is nowhere to be seen. (00:24:15)
Plot hole: No amusement park ride company would ever produce a prop scythe that was as sharp as depicted in the movie.
Other mistake: During the breakfast scene, Sgt. Botnick tells Andy he needs a trim on Wednesday, but he had just given him a haircut the previous day.
Character mistake: When Chucky is looking up the information about Andy on the computer, the word juvenile is misspelled "juvinile."
Other mistake: Chucky cuts Andy's Achilles tendon from under his bed. Throughout the rest of the movie, Andy should have a limp from such a severe injury. However, he has no trouble walking or running in subsequent scenes, nor does he show any signs of injury.
Plot hole: At some point during the war games exercise, headquarters would have eventually discovered Sgt. Botnick's body, and then they would have immediately stopped the exercise.
Plot hole: There is no way a military academy wouldn't teach their students the first rule of using a firearm: when you are given a firearm, you must always check if it is loaded and what kind of bullets it has. So there is no way Chucky could have switched the paintball shells with real bullets without someone noticing.