Continuity mistake: We see Sarah Jessica Parker well-dressed in red without a bra. When Bruce Willis remove her red robe, she's wearing a bra.
Continuity mistake: When the members of the brotherhood beat up Mani until he is dead, they pick him up above their heads. The tattoo on his torso appears to be on his right side, whereas in previous and following scenes the tattoo is on his left side. That shot is flipped.
Other mistake: Towards the end where they steal the chip, they are detected and about a million security guards are all running around, yet 30 seconds later, the only security guard is one man with a shotgun. What happened to their big army of security guards? (01:41:30 - 01:42:55)
Factual error: In the scene at the beginning of the movie as the 3 youths walk up the street, you can see current MA license plates, although the action should have taken place many years earlier. (00:01:30 - 00:05:50)
Continuity mistake: In the early scene when Harry walks across the street to confront the wounded robber on the street ("Did he fire six shots or only five?"), the shotgun used by the robber is lying several feet from the robber's hand, but when he reaches the robber, the camera shot shows the shotgun just a few inches from the robber's left hand. (00:13:00)
Continuity mistake: After Barry has jumped into the water reclaim the crown, he comes out of the water with a perfectly clean shirt, but in the next shot the blood is back on his shirt as expected. (00:22:50)
Continuity mistake: As Brian lands the plane down to Bangor, his headset is on in a frontal shot, but in a reverse shot it isn't. (00:47:05)
Factual error: A girl is playing with a Tamagotchi virtual pet in the scene set in 1994, but the toy was not released in Japan until 1996 (it wasn't officially available in the USA until May 1997).
Factual error: The geography around the VLA in New Mexico is actually relatively flat - in fact one of the reasons why the array complex is there is because the land is flat. The canyon in the film was actually Canyon de Chelly, in Arizona, more than 170 miles (270 km) away. But in the film, when Ellie goes to the canyon, the radio antennas seem to be right there, insinuating that the canyon is part of the VLA's magical desert scenery.
Factual error: Winter in Antarctica would not have a night and day as portrayed, with the amount of light changing so much during the course of 24 hours.
Visible crew/equipment: There's a scene in which someone goes into a phone booth to make a call. As the phone booth door closes you can see a reflection of the cameraman.
Visible crew/equipment: While in the pot field, just as the growers are about to shoot them with the laser sights, you can see a crewmember crawling by in the background. (00:44:50)
Character mistake: At the memorial service the principal says that it's been 39 days since 39 loved ones had died. But there were 40 students on the plane and 4 chaperones, making the total 44. Now 7 people got off the plane, which means 37 people related to that memorial service actually died, not 39. Two pilots would make up the numbers, but there would be flight crew too, which still leaves the numbers off.
Factual error: When Shorty is removing Jennings' memories in the beginning, the pictures shown are from a third person viewpoint. If they are his memories, shouldn't these be from Jennings' viewpoint? (00:06:40)
Continuity mistake: Eddie drives a 1957 Chevy convertible off the bridge. A scene showing the car being fished out of the water clearly has an older vehicle dangling from the line.
Suggested correction: The car pulled onto the bridge is absolutely a 1957 Chevrolet convertible.
Plot hole: When Nick confronts the P.I. and yells "Why are you following me?", he looks inside the car and see the file with his picture on the front seat. The P.I. notices this and turns the file over. After Nick grabs his gun, the P.I. jumps out on the other side, raises his hands in the air and tells him someone hired him and runs off. As the P.I. runs off, Nick yells "Who hired you?" as he stands alone next to the car. He then waits a minute and walks off. If he really wanted to know more information, he could have taken the file that was right in front of him on the carseat. It makes no sense that he is desperate for information about the strange events that are going on, sees this file on him, and yet doesn't even pick it up or look at it. (00:59:55)
Continuity mistake: Nick's character is eating an ice cream in the police car and eats the whole thing. When the shot changes to Simon's side, he's still got about half of it left.
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)
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.