During the scene at the Pont Neuf Bridge in Paris, close to the end of the film. They cut back and fourth between Jason Bourne on the roof of the hotel and CIA boss on the bridge. You see Bourne standing behind the letter sign on the hotel rooftop looking down at the boss through a scope, but when they cut to the boss, you can see the same hotel without Bourne on the roof. Bourne is supposed to be standing up, but can't see him at all, no silhouette or Bourne lying prone.