In the previous movies, Jason had a misshapen and asymmetrical face. His left eye was normal but his right eye was bulging and "dead"-looking. In this film, he has no left eye (as a result of his injury at the end of Friday the 13th: The Final Chapter), and his right eye appears perfectly normal.
When Tommy runs into the sheriff's office to tell him Jason's alive, the sheriff recognizes him and asks about Tommy's family, to which Tommy replies, "Yes, Jason killed them." This is inaccurate. Tommy's sister was not killed by Jason. Only his mother was.
(at around 11 mins) When Deputy Cologne comes in to the station, he is supposedly bringing in some take-out food. When he has to deal with Tommy and the boxes hit the ground, they sound like they are empty foam boxes.
The goof items below may give away important plot points.
When Sheriff Garris first encounters Jason, he shoots him in the mask; after his head snaps back, a hole is clearly visible. During Jason's struggle with Tommy then Megan, the hole keeps disappearing and re-appearing. In Friday the 13th Part VII: The New Blood, it is gone altogether.
(at around 39 mins) As Cort is driving the motor home, everything inside is moving back and forth, including a framed picture behind him. As Jason pulls Nikki into the bathroom, the frame stops moving, then starts moving again after Jason kills her.
Near the end of the movie, just after Jason breaks the boat in half and sinks to the bottom of the lake, you can see Jason has his hockey mask on. A few frames later, when we see Tommy swimming in the water, if you look closely, you can see that Jason has his hockey mask off, revealing his rotted face. Then when Jason grabs Tommy's leg and pulls him down, Jason has his mask on again.
When the sheriff first shoots Jason in the head at the camp after running out of shotgun bullets, you see a hole from the bullet hole in his mask next to his left eye. Once under water in the final scene, the hole is gone.