Continuity mistake: When the firefighters go to the house of the first backdraft "victim" you see that he has gone through the windshield of his car. But when we saw him opening his front door and getting hurled away from the house he didn't land anyway near the car.
Continuity mistake: After the bird of prey first fires on Enterprise, Kirk is thrown right out of his chair to his left and lands on the floor. The camera pans around the bridge briefly, seeing the rest of the crew staggering and holding onto things. In the very next shot Kirk is back in his chair shouting "back off, back off" and the crew back in their positions as if nothing has happened.
Revealing mistake: When John tries to stop the van while Maggie is driving, because he sees the small girl in the road, as the van screeches around the road, you can see the road is covered in tyremarks from previous takes. (00:20:10)
Factual error: In the scene where there is a train passing, the cars are marked "Burlington Northern." There was NO Burlington Northern until 1970, 7 years AFTER the shooting.
Continuity mistake: Watch the Mustang blow up at the beginning of the movie. It looks to be about an 88 GT convert. When it is shown after the explosion it changes to an 86. Two completely different looking cars. Check out the headlamps. (00:17:50)
Revealing mistake: During the beginning, as the newspaper headlines roll, the small text in the articles is actually the same text repeating itself over and over again, something like: "an investigation issued."
Continuity mistake: As William Lee types the "Report On The Assassination" in the café, letters that were visible in a previous shot disappear. (00:32:10)
Plot hole: Spoiler Warning. It turns out that Dan Merrick is actually Jack Stanton after a whole lot of reconstructive surgery to make him look like Dan Merrick. Everything is believable except that he has Dan Merrick's voice as well. He should have Jack Stanton's voice.
Continuity mistake: Cynthia walks alone to Joyce's house and also leaves by herself to clean the van. She speeds away from the house in order to clean the van in secret, but she somehow has her toddler son with her while she is cleaning the van. (00:46:45 - 00:52:16)