Continuity mistake: During the fight scene at Crystal Lake, Freddy stabs Jason's eyes, causing them to bleed very badly. But when Jason falls into the lake, we see him closing his eyes, and his eyes are perfect.
Visible crew/equipment: In the scene where Lori wakes up in the police station and follows the dropping blood, she turns a corner because she hears a little crying. Right after she turns the corner, the cameras show office windows. You can see someone sitting down and a cameraman on his knees.
Revealing mistake: When the drug "Hypnocil" is researched on the Internet, an article about the drug appears. If you pause the shot and read the article, you can see that it has nothing to do about Hypnocil. The article is about drug testing of students who engage in extracurricular activities.
Revealing mistake: As soon as the drunk kid sets Jason on fire there's a few quick shots of Jason's face but there's a perfect hole right through his head where his eye is supposed to be and you can see the night sky through it. Some people say it's a reflection off the goggles to protect the actor from the flames. Either way it's a mistake.
Continuity mistake: When the girls are at Lori's, just after Kia asks them if they think she needs a nose job, the lights flicker. When they flicker Kia is holding a compact in her left hand and she begins to close it. Both hands are up by her face but then the angle changes to a wider shot and her left hand is empty and on her lap and the compact is in her right hand as she places it on the sofa.
Continuity mistake: In the scene when Kia and Gibb meet Lori outside on the school bench after Trey's death look a few moments later, you see a close up shot of Gibb putting the cigarette towards her mouth and almost reaches her lips, in the very next shot Gibb has the cigarette down in her hand and then a second later she then puts it to her mouth.
Continuity mistake: In the fight scene on the pier, just after Freddy has sliced off Jason's fingers, Jason blocks the machete, Freddy slashes him with the glove and then cuts Jason's chest with the machete and raises the machete for a downward blow. They are now standing face to face. However, when Freddy makes this cut, Jason's back is all of a sudden turned, enabling Freddy to cut his leg from behind. There was no time for him to turn around between cuts.
Continuity mistake: When the teens enter the mental institution to get the dream suppressant drug, it shows a security guard drawing his pistol in alert to an intruder banging on a door. The next shot cuts to show the response of two teens hearing a single shot fired, and then cuts back to show the security guard under the door with four big dents from Jason and two bullet holes. The holes are located at the top right hand corner of the door and the other near the door handle.
Continuity mistake: When Lori explains she haven't had much sleep lately, Kia says "Lori, you had to sleep at the police station.". If you look at Kia's purse's straps you can see some of Kia's dress sticking up between the straps. When it cuts the piece of her dress no longer sticks up between the straps.
Continuity mistake: In the end of the movie when Jason comes through the water stabbing Freddy with his own glove, you can see the spikes only coming out of Freddy's chest. When it cuts to Freddy falling to his knees, the whole fist and parts of his armwrist suddenly has gone through his chest.
Deliberate mistake: When Jason throws Freddy to the wall in the burning house, you can see a window on the wall. Now, the distance between the window and the corner of the wall is about five feet. This gives Freddy space enough to hit the wall and not hit the window. However when Jason picks Freddy up you can see the distance has increased to about one feet. It's like they've put in an extra window where there should be a wall instead.
Plot hole: During the first fight scene between Freddy and Jason in the dream world, Jason tosses Freddy into some pipes which causes water to spray everywhere. When Jason is about to attack Freddy and stops to back away from the water, it is explained that Jason is "afraid" of the water. While logical on paper, this makes absolutely no sense with the rest of the Friday the 13th movies and an earlier scene in Freddy vs. Jason. Jason has on many occasions ventured freely into Crystal Lake to kill his victims in earlier movies, and in this movie he walks all the way to Elm Street in the pouring rain. Surely if he was afraid of water he'd not have completely submerged himself in a lake, and would have taken shelter under a tree until the rain storm passed.
Continuity mistake: In the scene where Linderman and the deputy is watching Freeburg throwing all the Hypnocil pills down the drain, they are looking through a glass. Then you see Jason coming up from behind lifting his left arm with the machete reflected in the window. When it cuts he lifts his arm again but this time it is his right arm.
Continuity mistake: In the scene where the teen tranquilizes Jason and gets cut in half, we see the two parts of the body in the left side of the hallway. After a few scenes, when the camera gets a close-up of the bodyparts, we see one in the left side of the hallway and the other one in the right side.
Factual error: Right before the second boy gets killed he wakes up after having a dream of Freddy and sees his dad sitting next to him. When the boy taps his dad lightly his head falls off and we then see Jason standing there. In order for this to have happened, Jason would have had to unbutton the dad's shirt, chop his head off, put it back in place, and rebutton his shirt without getting any blood anywhere on the body and without the dad putting up a fight. Also Jason waits until after the boy wakes up and sees his dad dead before killing him. Wouldn't Jason just kill him in his sleep like he does to the girl in the cornfield later on in the movie?