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.
Continuity mistake: During the car chase in Paris, the sun shines when the camera films the front of the car Bourne is driving, but it's grey and gloomy when the camera films the rear of the car. Changes back and forth throughout the entire car chase.
Continuity mistake: In the car chase scene, the windscreen wipers on the Mini change from being on, then to off, then back on again throughout the whole chase. (00:52:42)
Continuity mistake: After Bourne dyes and cuts Marie's hair, she is left with long tendrils at her temples. He brushes them away when they start kissing. But the next morning, when Marie wakes up in bed, all of the front of her hair is cut short.
Continuity mistake: When Wombosi gets assassinated, the shot changes to a view of the sniper's scope. The glass on the window is not broken, even after a bullet was fired through it. (01:03:44)
Continuity mistake: In the scene where Jason Bourne first wrestles with the boat's doctor/captain, the man shows Jason the cylinder that was in his hip and asks him why it was there. Jason grabs it and his hands are clean, then in the next shot as the medic is still holding him there is blood all over Jason's hand as Jason continues examining this cylinder, then the blood disappears again.
Continuity mistake: In the Paris Gare du Nord shot where he is to leave the bag, when they pull up to the station time is 16:15 in the first shot of the watch, then cut to car he gets out, time is 12:00 then inside time table show around 16:30 unable to see how long up, but it is no longer 12:00 then camera moves around him and cut and a time table for track 12 shows 18:26 He looks at the timetable pondering if he should leave Marie and now the timetable for track 12 shows 14:37 and the clock in the background 14:29.
Continuity mistake: As Bourne is running through the embassy, the red bank bag alternates multiple times between being over his right shoulder and his left.