Revealing mistake: Near the end when Jason throws the hammer at the girl, it sticks to the damaged part of the wall after it hits. But it's just against the wood with the flat top, there's nothing to hold the hammer there and it's only hit the wood on the other side of the wall. They probably used a magnet to attract and keep it there for safety reasons.
Plot hole: When Jason is going next door to chase after Trish, he pulls Jimbo's body down from the doorway and begins walking towards Trish's cabin. He is seen walking by himself. However in the next scene, he throws Rob's body through the window. There was no time for him to go back and get the body.
Plot hole: When Jason first wakes up in the morgue, he kills two hospital employees inside the hospital (a semi-public place) and leaves them there. Later in the movie, Rob Dyer (the hitchhiker)in trying to convince Trish Jarvis that Jason Voorhees is still alive, he says that two hospital employees disappeared. Their bodies were not discovered in the middle of a hospital?