Visible crew/equipment: Right at the end of the car chase, the yellow van in the pile-up is flipped over by some kind of large metal lever in the undercarriage. This is seen from the last 2 angles of the crash. (00:52:45)
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)
Visible crew/equipment: When Eamon is running away with Marie and his kids, the camera passes behind the car and a crew member is reflected in the trunk.
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)
Factual error: When Jason asks Marie for the pay phone number in front of the Hotel Regina, she gives him a 7-digit number, 616 2468. A French phone number would be 8 digits, not including the (0)1 prefix. (01:01:35)
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.
Revealing mistake: Just as Jason is returning to the car from the train station after dumping the bag in a locker, spectators can be seen watching the filming, which was apparently done on the sly and without consent. Nonetheless, the onlookers did notice the film shoot and followed the actors' actions, who are not doing anything in the scene to draw attention to themselves. Watch the black man to the left of Jason in the background, he follows the scene and his head turns as he watches. Then look behind Marie right after that and there are 2 or 3 people watching as well, in the background. This is very visible and very distracting. (00:50:50)
Other mistake: After Jason rams the man through the railing at the top of the stairs, he puts in a new clip. As he falls through the air, he shoots the other guard once. Then, he puts in a new clip when he rises after the fall. After one shot?
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)