Plot hole: When the film opens, Jason is bound and restrained in an empty room. After killing the six security guards and appearing in the hallway, he chases after Rowan with a machete. Where'd he get this? All the guards had guns, and the rest of the room was completely barren. [Apparently, there was a cut scene (unfortunately deleted scenes weren't included on the DVD) showing Rowan with a box of Crystal Lake newspaper clippings and other Jason material/evidence, and his machete was one of the items in the box. Still a mistake due to the empty room (ropey editing), but that's the reason.]
Plot hole: When the Grundel explodes near the end, Rowan looks out the window to see Uber Jason floating towards the rescue shuttle, only to be grabbed by Brodsky who happens to fly sideways at a high rate of speed. Now provided it's feasible that Uber Jason can survive an immense explosion, how Brodksy not only survived the explosion but managed to wind up away from the spaceship and far enough off to the right so as to catch Jason in mid-space is beyond me.
Factual error: When Jason is outside the ship and punches the hole to get back inside, the crew rush to the door and close it because the lack of pressure is causing them to be sucked out of the ship. They go through several rooms and close multiple doors. Yet when Jason rips through the final door, there's no sudden rush of air, no loss of cabin pressure, even though there would be a continuous path to the broken outer wall of the ship.
Continuity mistake: In one shot we see the thick green blood dripping off of the autopsy table which Jason is on, and there is plenty of blood running down the side. In later shots when Adrienne turns around and looks at the table, the amount of blood dripping down the side of the table has decreased, and the amount changes in following shots as well.
Plot hole: When Professor Lowe calls Dieter Perez to tell him about his findings on Earth 1, Perez makes note that one of the viables was named Voorhees and deduced it was Jason Voorhees. How did Lowe know it was named Voorhees? 1) Rowan at the beginning acknowledged she had yet to prep the chamber which means no paperwork. 2) The students found no paperwork when they found the chamber and had no time to look for paperwork once they realized they needed to get Rowan to a lab to save her right away. 3) Rowan did not give him Jason's name when she first woke up. This is obvious in the scene after Lowe talked with Perez he was talking to Rowan and she brought up the story about Jason and he acted like he never heard the name before. So there is no way for Lowe to know Jason's name for his report to Dieter.
Continuity mistake: At the beginning they show a close up of Jason, the skin around his eyes and ears (around the outside of the mask), are flesh colored and looks like normal healthy skin. When Adrianne takes his mask off during the autopsy they skin is grayish like it's decaying.
Continuity mistake: When Rowan is stabbed by Jason she slides down to the floor and freezes sitting up. She remained undiscovered and undisturbed for over 400 years until the scientists find them. So how did she end up lying on her back covered up by what look like exhaust tubes? Aside from the unlikelihood of no-one stumbling across her for all that time.