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.
Plot hole: In the institute, Will's friend gets out of his room to get the guard's keys. He couldn't have gotten out of his room because there isn't a handle or door lock inside the room.
Plot hole: The sheriff orders a 24 hour roadblock on the town, yet the van has no trouble driving to Crystal Lake.
Plot hole: Linderman didn't know who Jason was after the rave massacre, calling him a "psycho in the hockey-mask", but later in the film when Stubb's is telling them (Will, Lori, linderman, Freeburg and Kia) about thinking Jason is a copycat, Linderman suddenly acts like he knows who they're dealing with when he didn't before. "I've seen what he can do, he's the real Jason."
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.
But this is not the way how Jason works - he doesn't play games as Freddy does; the moment he sees the person, he just kills. Killing of Blake and his dad was way off Jason's Modus Operandi.