Corrected entry: 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.
Correction: Water wasn't Jason's weakness until and unless he was dreaming, and it wasn't exactly water, it was the fear of drowning, which was his original death, and Freddy exploited that weakness to torment him in the dream-world.
Correction: Jason is only afraid of water in his dreams.
Corrected entry: Jason looks different here. This takes place after Jason Goes To Hell where he had bloodied hot pink skin, silver welded on hockey mask, dark blue boiler suit. Yet here he's wearing tattered clothes with black gloves, the original looking hockey mask, and is black skinned just like he was in Friday Part 6.
Correction: I think this mistake is dubious at best. The canon of the "Friday the 13th" series is already pretty sloppy with the films contradicting one-another, and this film indeed also contain ideas and notions that contradict both franchises. (Not the least of which being that Jason was literally dragged all the way to hell at the end of "Jason Goes to Hell", but is merely "asleep" just beneath the ground at the beginning of this film.) I don't think it's a stretch to say this film is more of an "alternate universe/what if?" situation, and not really a direct sequel to "Jason Goes to Hell" and "Freddy's Dead," and thus minor cosmetic differences shouldn't really be considered mistakes.
Corrected entry: 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.
Correction: It's explained at the beginning of Jason X that he has ability to regenerate cells rapidly so it's possible he has fast healing for his eyes as well.
Plot hole: 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?
Suggested correction: Maybe Jason set up the dad to freak out Blake. His dad left him on the porch and we don't see Jason actually kill him.
Plot hole: There's no way Jason could decapitate Blake's father the way he did without also decapitating Blake, who was sitting next to him sleeping.
Suggested correction: Maybe he set him up that way? His father did leave before this happened after all.
Other mistake: Towards the end after the kids wreck the van, Kia points to a sign for Crystal Lake. That's where they are supposed to go but they go the other direction, away from Crystal Lake.
Suggested correction: They were still heading for the camp, which is where the fight takes place.
Other mistake: Jason drowned in 1957 yet Stubbs says he drowned in the 1930's.
Suggested correction: Stubbs actually mentions that Jason drowned in 1957. He said it while he was talking to the teens at the table.
Revealing mistake: When Freddy drops the large boiler on top of Jason during their fight in the warehouse, the boiler is made of cardboard or some other lightweight material because it doesn't land very hard and it even bounces a bit.
Suggested correction: It is also a dream which means anything can happen.
Freddy was trying to kill Jason. Why would he drop something on top of Jason that was too light to crush him?
Correction: This is in the dream world, the unconscious mind. It could be that Jason is very well afraid of water but when awake can stomach that fear and move on. In the dream world however there is only the fear. It is the same way that someone might be afraid of spiders in real life but can walk past a spider no problem yet still have nightmares about spiders later.