(at around 1h 9 mins) When Jessica first picks up the note out of the box crib, it says "I have what you want...", when Steven reads the note, it says "I have your baby..."
(at around 36 mins) When we first see Jessica while she is talking to her mom on the phone, her baby has no hair. Then when she visits her mother's house a little later (at around 41 mins) the baby has a full head of hair and is bigger.
(at around 16 mins) On the American Case File show, they show pictures of the coroners that were killed. The picture of the assistant coroner is just a still from the previous scene.
(at around 2 mins) When Agent Marcus replaces the light bulb, she places the dead one on the ladder. She folds up the ladder and leans it against the wall without removing the bulb, and it does not fall.
(at around 27 mins) When Deborah and her boyfriend go into the tent, their shadows show her taking off her shirt and tossing it aside. In the next outside shot of the tent, her boyfriend is once again shown taking off her shirt.
Around 16:10 When Jason-coroner grabs the other coroner by the back of the neck, the latter lets out choking sounds even though the throat is located in the front of the neck.
(at around 7 mins) Obvious dummy or mini when Jason is being blown up. He suddenly stiffens when the bomb is dropped, and the machete is protruding from his open hand.
(at around 1h 5 mins) Steven is obviously not bound by real handcuffs in the police station, because when he jumps up and passes his hands under his legs, he spreads his hands a lot wider than real handcuffs would allow. If you look closely, there is just a piece of string binding his hands.
(at around 1h 6 mins) When Jason (in Robert's body) is shot in the head at the end of the hall, a close up reveals the bullet hole to be obviously just makeup.
(at around 7 mins) When Jason is being shot by the FBI, it's just the same shot being repeated from different angles.
(at around 31 mins) When the girl is impaled with a post in the tent, a large, bloody gash is already visible running up her body in the exact spot that Jason thrusts the post upwards; before he actually does it. This pre-cut on the dummy was done to give the pole a straight, clean line to move up in so it would look good in the movie.
Prior to possessing the sheriff's deputy, Jason (in the coroner's body) is seen shaving the deputy's mustache. This seems to make no sense for Jason to take this action, especially since the coroner had a mustache.
It's never really established how Creighton Duke knew about the FBI's operation to trap and kill Jason. The FBI would have undoubtedly kept knowledge of the operation limited to its own people, and no one outside the FBI should have known about it.
(at around 1h 1 min) Reflection of cameraman in passenger side window when Steven and Jessica get into the car.
(at around 1h 20 mins) When Jessica attacks Jason from behind, there are obvious steps and a platform that she runs up onto to meet his height.
The wire controlling Jason's detached head is visible at the top of the screen as it falls.
It appears no one even did the slightest bit of police work in the murder of Jessica's mother, if they had they would have seen evidence that Steve's story was true. Like evidence of someone going out the window and the cop's fingerprints on the knife.
It's never really established how Creighton Duke obtained the in-depth knowledge about Jason, including how he was able to possess bodies and the method to destroy him.
After Steven breaks out of prison, he goes to Jason's home. Then Jessica's boyfriend shows up talking on the phone and he says he will ask Jessica for permission to shoot their show at Jason's house. He should know that Jessica doesn't know she is a relative of Jason.
After encountering Jason inside the house, Agent Marcus escapes on foot with him chasing her, where she leads him to an area in the woods where her fellow FBI agents are waiting for him. Once he arrives, they turn on flood lights and begin shooting him. It would have taken them a while to set up the equipment (e.g. flood lights) to wait for Jason, and he could have discovered it (and killed the agents on scene) long before he attacked Agent Marcus.
In the scene where Jessica is in the shower crying and the power goes out, she gets out, puts on a white t-shirt and goes walking around the house. When she walks through the garage door and grabs a hammer, there is blood on the front of the t-shirt (right at or a little lower than her waist and looks like someone grabbed the shirt with a bloody hand). Where did it come from? She didn't run into anything or anyone. [There's a deleted scene showing her step on a piece of glass. She gets blood on her hands when she pulls the glass out, then presumably wipes her hands on her shirt. Still a mistake, as removing that scene means the blood appears from nowhere, but there's the reason.]