Continuity mistake: In the scene where all the Treadstone agents are being contacted, we see Sagrada Familia in Barcelona. In the first shot of the building we see cranes standing next to it. In the next shot, the cranes have disappeared.
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.
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.
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?
Continuity mistake: When Bourne gets the box from his numbered bank account, the bank clerk carries it by holding its handle. Then he puts it on the table tipping it over to the side, so Bourne can open it. Thus the ingredients (especially the heavy weapon) should all be laying on the right side, what used to be the bottom of the box. But when Bourne opens it, everything is nicely arranged.
Continuity mistake: When Wombosi is assassinated by the other agent he is shown walking down the stairs with glasses on and a turtleneck sweater. He also has another man following him. Then the next shot shows Wombosi (or a stuntman) standing in front of the window with a leather coat on and no glasses. He is obviously not walking anymore and the man behind him is nowhere to be seen.
Factual error: Throughout the movie, there are countless references to the incident early in the movie at the U.S. Embassy in Zurich. Neither the U.S. nor any other country maintains an embassy in Zurich. The capital of Switzerland is Bern. Since most of the characters in the movie work for the U.S. government, they would surely know the difference between an embassy and a consulate.
Continuity mistake: When Bourne approaches Marie about a ride, they talk across the top of her Mini. First, there is lots of snow on the car's roof. Then, there isn't.
Audio problem: When the first assassin runs out of bullets shortly after coming through the apartment window, his gun makes a series of rapid clicks as if dry firing full-auto, but real guns, even full-auto ones, don't keep on clicking when empty. It should either make a single click, or a nearly inaudible one.
Continuity mistake: When Bourne blows up the tank at the farmhouse, the wide shots show a solid wall of black smoke. In the closer shots there's nowhere near as much. The smoke in the first shot must be coming from the explosion, and in the closer shot we're looking right at the destroyed tank, so it can't be due to different angles.
Continuity mistake: In the scene at Treadstone HQ when they are looking at the footage of Bourne and Marie in the alley, Chris Cooper is wearing a short sleeved blue oxford dress shirt. When they zoom in on Marie to present her bio, Cooper is wearing a long sleeved shirt.
Continuity mistake: When Jason and Marie are in the car prior to the car chase they have a conversation with camera angles switching back and forth in the car. From shot to shot the window glass is alternately covered with a lot of rain droplets, a few rain droplets, and even completely dry.
Continuity mistake: In the part of the embassy scene where Matt Damon starts clobbering security people, the Marine's hat falls off no less than three times.
Continuity mistake: When Bourne is escaping from the Embassy, he drops the bag, which hits some metal thing on the way down, making it wobble to and fro. The camera cuts away while it's still moving and we see the marines coming upstairs. When Bourne climbs under the fire escape, we can see down to the ground and the metal thing's stopped moving. All well and good, except after the marines leave Bourne looks down, and in that shot the metal thing is moving again, then stops - obviously the rest of the shot we saw before.
Continuity mistake: In the scene where Bourne is watching Conklin arrive on the Pont Neuf in Paris. The very first time Bourne is seen looking down at the bridge from the roof there is a long row of traffic all along its length. There is a scooter heading the direction of the traffic. Bourne gets his scope out and follows the scooter, yet from that moment on the line of traffic has magically vanished. You see the scooter through the scope about 2 seconds after you can see it on the bridge, and it would still be going along beside the traffic, but the traffic is gone.
Factual error: When Bourne arranges the rendezvous on the bridge (Pont Neuf) the time is scheduled for 5:30pm. At this time, in winter, in Paris, it would be dark, but the scene is in daylight.
Continuity mistake: In the scene where Jason steals a grey Ford Sierra, when Marie walks from the phone booth to the car (Jason is taping the window) she passes a red Ford Fiesta and there is a grey Renault Laguna behind it. The car they are stealing is out of shot. When they drive off their car is suddenly on the spot where the Renault was.
Visible crew/equipment: When Bourne is escaping from the Embassy and standing on the fire escape ledge, the safety cable for the later climbing scenes is clearly visible on the ledge around the corner to the right.
Continuity mistake: When Wombosi is shot, the bullets come through the bottom of the window which has bars. From the outside, we are shown that the shots go into the top of the window, and there are no bars on it. There are also curtains and fabric which disappear.