Visible crew/equipment: After Bourne and Marie get to Paris, Bourne is sleeping and Marie awakens him. Shortly after he gets out of the car you can see a crew member's head reflected in the rear right window. (00:34:25)
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)
Visible crew/equipment: As Eamon is getting ready to leave with his children after Jason kills The Professor, a cameraman's legs are reflected in the back of his car just before he says the line "I'm not waiting, Marie". (01:30:35)
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.
Visible crew/equipment: When Bourne is scoping out the bridge he is supposed to meet Chris Cooper on, a piece of camera equipment is showing on the right hand of the screen.
Visible crew/equipment: Hanging on the balcony of the embassy, Bourne's stunt double is very noticeable because he is much older and has longer hair.
Visible crew/equipment: When Bourne exits the car and walks to the train station to leave the bag, he is replaced by an obvious stand-in.
Answer: He taped the door edges so they wouldn't leave fingerprints on the car.