Continuity mistake: When Jason is cutting Marie's hair in the hotel room, his watch is on his left wrist. When he and Marie begin to kiss, in this flipped shot Jason's watch is on his right wrist, his moles have changed sides, and the hand-held showerhead behind them is backwards as well. Next shot his watch is back on his left wrist. The flipped shot has nothing to do with the small bathroom mirror. (01:00:56)
Continuity mistake: This is the scene where Jason is on the fire escape platform in the consulate in Zurich. Before he goes down below the platform we see that the platform is cleared of all the snow. Then moments later, when security guard opens the door and Jason is under the platform, the top of the platform is fully covered with snow again. (00:23:46)
Plot hole: In Paris, why does the assassin go to the ridiculous amount of trouble of swinging into the room on a rope with a machine gun when he came in from the lobby (as proved by the dead woman downstairs)? Alternatively, if his intention was always to surprise Bourne by coming in through the window, why venture downstairs at all? (00:44:07)
Nicolette: He killed our man.
Conklin: What, in the apartment?
Conklin: Well, you got to clean that up.
Nicolette: No, I can't clean it up; there's a body in the streets.
Nicolette: There's police, this is Paris.