Continuity mistake: In the opening scene, Mort closes the door of his jeep before he goes into the hotel room. You can hear the sound of the door closing and it's visible in the rearview-mirror. As the camera moves out of the room, the jeep door is completely open. (00:02:05)
Suggested correction: The door just didn't actually catch. I've had cars like that, especially during the winter.
Given that we see it stay closed for almost 4 seconds and hear it catch, it's a valid mistake.
If you've ever lived where it snows a lot, you'd know that door catches accumulate moisture (ice) and can open slowly, as it did in this case.
Continuity mistake: In the Moscow car chase, Bourne's car is hit from the driver's side by a patrol car. The driver's side window breaks. In the next few shots, you do not see any broken glass on Bourne. In the very next shot the car is not damaged on the driver's side. (01:25:25)
Plot hole: In the scene where she goes to her house after escaping there is no police tape on the front door even though it is a crime scene. Earlier the police searched and taped her office - it only makes sense that they would do the same to her house.
Continuity mistake: When Bourne is talking to Firsch, the gun he is holding changes from a Glock in the shots facing Bourne, to a SigPro when the shots face Firsch.
Factual error: The solar panels (or mirrors) are facing away from the sun. The sun's position can be estimated from ground shadows and object highlights and the panels are facing in completely the wrong direction. (01:11:40)
Continuity mistake: When Frank Walker and Casey Newton get into Frank's bath to escape the robots, Frank gets in on the left and Casey gets in on the right. They get shot off but when they land in the swamp, Frank is on the right and Casey is on the left.
Factual error: During the custody hearing, the Maryland flag in the courtroom is upside down. The rule for a Maryland flag is "black and gold, top of the pole," this flag has the red symbol at the top.
Visible crew/equipment: When Alan is struggling with Barbara on the drawbridge, the shadow of a camera/operator is on Alan's back as they get near the car. (01:30:30)
Revealing mistake: When the body of Miss Lefferts is being viewed, the 'dead' girl blinks slightly. (00:34:35)
Continuity mistake: When Frankie is about to receive the first stigmata (when sitting in the bath), a pigeon suddenly flies up. When she takes a piece of a feather that flew into the water, you can already see stigmata marks on her right-hand wrists.
Continuity mistake: In the scene where Eddie Murphy is going into the crypt, he takes one of the lit torches. While they are trying to escape the skeletons, the door to the crypt closes and locks. When they show the shot of his son outside, you see two torches again. When he gets the doors open and they leave, you see one.
Factual error: There is no possible way to cause a power line to drop from its support pylons and hit a person on target. These wires are fastened extremely securely, designed to withstand extremely high tension through all kinds of weather, and they are not equipped with some sort of explosive charges to release them.
Deliberate mistake: Despite taking place for at least three years (prior to the arrival of Thomas) in an isolated post-apocalyptic setting, the boys in the Glade have professional looking hairstyles, not the least of which are Minho and Gally, who both have short hairstyles that look evenly cut and professionally maintained.
Continuity mistake: There is a scene in which a ghost shoots harpoons through the back door of the Mystery Machine. In the next shot, the harpoons are gone, and when the van gets back into the city you see a shot of the back and there is no damage whatsoever. (01:03:20)
Continuity mistake: At the end of the movie when the mob guys come to the boat house to move the body, Barry the Blade shoots a raccoon with his gun which has a silencer. But, later when Reggie shoots the neighbor's alarm system with Barry's gun, it does not sound like it has a silencer anymore.
Suggested correction: The silencer fell off the gun when "the blade" tackled the kid and Reggie. They show the silencer falling off the gun into the leaves.
Continuity mistake: In the scene where Thora Birch's character goes to a café with her psychologist, the psychologist takes a bite of a cake and puts it back on the table. In the next scene, the cake has not been touched.
Continuity mistake: When Sy is following Nina and Jake after he put the picture of the husband cheating in with Jake's pictures, the cars pull over to the side of the road. If you watch when they pull over, you see that they pull over next to a down sloping hill that is nicely green with grass and a few sporadic trees. But when they show Sy's car in the rearview mirror, you see that they are now pulled next to a large up sloping hill that is covered in leaves, dirt, and a lot of trees. (00:53:40)
Factual error: The movie is supposed to take place over the course of a single summer. In one section of the film, Bobby is reading a story about VP Nixon's recent Presidential nomination, which took place in 1960. Later, he is reading a story of Maury Wills base stealing record, which occurred in 1962. (00:25:00)
Continuity mistake: In many places in the movie, a cat noise is heard even though the cat's mouth is quite obviously not open or the cat is licking its face.
Plot hole: During the end the murderer is thrown out the front window of the building. The students leave the building through the front door, but yet there is no body, and that doesn't seem to bother them!