Continuity mistake: During the car chase there is a shot of Bourne steering frantically. In the centre of the steering wheel is a Mini badge. Cut back a few moments later and the badge has changed to a Cooper badge. (00:51:15 - 00:52:05)
Continuity mistake: At the beginning of the car chase, the red car has a burnt out leftside tail light. For the remainder of the chase, it's working. (00:52:57)
Continuity mistake: When Jason is climbing down the side of the embassy, there is a car in the snow. When the camera cuts directly to him, then back to the aerial view, the car is gone, there are no tracks and it isn't snowing hard enough to cover the tracks.
Continuity mistake: When Bourne is escaping the embassy, he has to scale down a wall below a broken fire escape. As he is inching his way to his right, towards the corner, the shot changes to one from below, and he is suddenly about six feet lower than he was the moment before (there is a curved pipe jutting out of the wall that allows you to easily judge his actual position.) (00:23:33)
Continuity mistake: In the scene where Bourne is moving up the stairs in the embassy, as he approaches the 5th floor you see the legs and feet of someone either standing, or perhaps an evacuee. In the shot immediately following, the person is gone. (00:21:30)
Continuity mistake: When Jason is viewing the CIA agent from the roof of the building, Jason is standing directly behind the big letters of the name. There's a cut and you can see the agent on the bridge and in the background the building on which Jason should be standing, but Jason is NOT there. If the actor were in this clear shot, he would easily be visible. At the next cut he's back again behind the big letters. (01:36:33)
Continuity mistake: When Jason goes into the bank in Switzerland for the first time, he puts his hand up to the identification plate, and then he takes it off. It reads him and allows him to go in, but the next shot shows him taking his hand off the reader again. (00:15:12)
Continuity mistake: At the beginning of the film, Matt Damon has a flashing light attached into his chest, then we see it's a big red battery pack attached to a light, at the end of the movie, when he is having flashbacks, the battery pack and the light are not on the wet suit he has on, and the light is not flashing when he was in the water. (00:01:46)
Continuity mistake: Throughout the movie, Marie is wearing nail polish. When Jason and her are talking in the car when he returns from the train station, however, there is a shot of her having Jason's money in her hands. She is not wearing nail polish and her fingernails are longer - someone else's hands or the scenes were shot out of sequence and she had longer nails and nailpolish.
Continuity mistake: As Conklin walks on to the Pont Neuf, the French "associate" watches him directly and then speaks into his collar (a very obvious tip-off as to what's going on). But as Bourne watches this happen, the Frenchman has his back to Conklin, without adequate time to have turned around.
Continuity mistake: After Jason kills The Professor, we see Eamon walking to his car with his children and opening the right side passenger door. We then cut to a shot of Marie and then back to Eamon. His car's boot is now suddenly open as well as the right side passenger door, but we never hear him open it during the shot of Marie. (01:30:20)
Continuity mistake: In Bourne's Paris apartment, Bourne takes off his orange jumper and leaves it on the desk. When he kicks Castel over the desk, the orange jumper is knocked to the floor. After Castel goes out the window, the jumper is back on the desk again.
Continuity mistake: When Bourne is on the phone with the French hotel asking whether his identities are checked in there, his right hand changes from holding passports to holding the phone between shots.