Revealing mistake: When Jason is escaping from the embassy building the railing comes away from the wall. The man hanging on the building by one hand when the red bag falls is obviously a stuntman because he has curly hair. (00:23:32)
Continuity mistake: When Jason is on the 5th floor of the embassy looking for an exit he is holding a walkie-talkie in his right hand, wearing white earphones and carrying the red bag on his left shoulder. In the next shot the white earphones and walkie-talkie have disappeared and the red bag is suddenly on his left shoulder. The bullet hole pattern in Jason's back has also been reversed as if the scene had been flipped. (00:22:32)
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.
Character mistake: The man in the morgue says in Yoruba "'I told you so, your head is not correct," not what they interpreted.
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.
Audio problem: When The Professor is driving in the BMW, you can hear the transmission engage the next gear before he is seen completing the gear change. Shortly thereafter, you hear another gear change, but The Professor's hands are nowhere near the shifter (he's reading his orders on his cellphone).