Revealing mistake: When Jason breaks his hand through the door it's really strange how his hand makes a perfect square on the broken door. Telling that the door was already broken and then repaired loosely for the stunt.
Continuity mistake: In the film Jason kills the guy in the sauna with a hot coal into his stomach, and there's no blood. When Jason leaves you can see the guys chest and now it's covered with blood. (00:28:45)
Continuity mistake: When Jason is holding Eva in the air, he lifts her up higher towards the ceiling, but in the shots of her feet, they stay in the same position.
Continuity mistake: Crystal Lake goes from a lake surrounded by land in previous installments to suddenly having the space for a small yacht and a channel that feeds right to the open ocean.
Factual error: Jason put Shawn's dad up against the ships wheel. Dead bodies can't stand up.
Revealing mistake: When Sean and Rennie run through the two glass doors leading down into the New York subway system, you can see Jason's shadow on the wall as he stands off camera and waits for his cue to walk on screen and kick his way through the glass doors. (01:19:25)
Continuity mistake: When Rennie and Sean are on the ladder in the sewer Rennie's position changes between shots. (01:29:50)
Revealing mistake: During the part where J.J. goes down to the boiler room to play her guitar, Jason sneaks up behind her. She screams and runs down more stairs, and then right before Jason kills her, as he lifts the guitar to hit her, in the lower right hand of the screen you can see the blood coming out of the guitar before it hits her. (00:21:25)
Other mistake: Rennie shouldn't have been able to get on the boat at all. Being high school students, they would need a permission slip signed by their legal guardian to board the ship, just like any field trip. And, it's obvious that Charles would not sign one allowing Rennie to board. He definitely voiced his objections to the female teacher. Rennie can't make that decision on her own as she did.
Continuity mistake: Rennie's visions of Jason as a boy change their appearance constantly throughout the film. At some points he is bald and deformed, much like how he was in the original film. At other times he appears as a normal, non-deformed boy with a full head of brown hair. At some moments he even appears as a mix of both (with a deformed face, but a full head of hair). This inconsistency is never explained or even acknowledged.
Factual error: In Manhattan, you can't just climb into a sewer tunnel. They are barricaded, meaning the only people who are allowed down there are city workers.