Factual error: During the chase in Moscow, just after Bourne is shot in the shoulder, the Russian assassin runs down a subway entrance, but this is really at Berlin Alexanderplatz. In the background is the Kongresshalle, located just next to the Alexanderplatz, and there is in fact a U-Bahn entrance opposite it.
Factual error: When Bourne is tapping into the phone of the American consulate investigator, the display of his Siemens cell phone shows Pamela Landy's phone number as an incoming call, giving him the option to reply or reject the call. But at this point, they have already been talking for a while.
Continuity mistake: During the scene where Jason Bourne interrogates the girl from Paris in a tram tunnel, her hair keeps changing from camera angle to camera angle. In one angle, it's off her face; in another angle, it's disheveled and covers the right side of her face.
Continuity mistake: In the chase scene toward the end, both Bourne's and the assassin's vehicles are racing down a tunnel. Both of them run several cars off the road while passing them, which should block traffic behind them. Instead, in one long shot of the tunnel, a ton of moving cars can still be seen directly behind them in the tunnel as if traffic was completely normal. Furthermore, even if there was room to drive around the obstructions, nobody thinks it's a good idea to back off from two cars smashing into things?
Factual error: When Bourne drives from Naples to Berlin, he wakes up from a nightmare at Dreilinden, just outside of Berlin (easily recognizable by the bridge in the background). A few scenes later he is seen driving through an Alpine landscape which he should already have passed long before getting to Germany.
Factual error: The sirens used in Munich and Berlin are not German sirens, the ones in Munich sound like from another European country and at the demonstration in Berlin an American siren can be heard.
Other mistake: In the scene where Jason drops from the bridge to the boat, you see him grab his left leg/knee in pain. But throughout the rest of the film, you see him limping on his right leg.
Continuity mistake: When Bourne makes the call to Pamela Landy from the rooftop, we hear him talking about Nicky. When the camera switches to her, we see she is across the room, away from Pamela. In the next shot, with the view from outside the window, she is standing right next to Pamela, and then moves back again in the next shot.
Other mistake: When Bourne is looking up the address of Hotel Brecker on the website, the street is spelled Kurtürstendamm. It should read Kurfürstendamm with an F. The English translation of this famous street's name is "causeway of the electoral princes"
Factual error: After Jason escapes from the interrogation room at Naples airport, he uses a remote unlocking device to unlock a car. The car opening is an old E28 BMW 5 series which was never equipped with remote unlocking functionality.
Factual error: When Jason Bourne travels from Berlin to Moscow, the train shown arriving in the station is what Russians call an "elektrichka" - a local commuter train. It's about like having someone travel from Seattle to Chicago on and arrive on the El.
Revealing mistake: Early in the movie during the scene which Jason Bourne is being detained, the person from the Consulate while questioning Jason Bourne gets interrupted by a cell phone call. He has a Hand Spring PDA/phone and during the phone conversation you can see a red light flash on top of the phone. If you own one of these phones you know that means you have no cellular signal. How could he be having a phone conversation if he has no signal?
Continuity mistake: The damage to the taxi in Moscow is constantly changing. Noticeably a massive spider crack in the windshield that disappears in the wide angles.
Continuity mistake: In "Identity", Marie has a tattoo on the upper right shoulder portion of her back. In the beginning of "Supremacy", she is walking in a bikini top. We see her back for a few seconds and there is no back tattoo, only the one on her right arm.
Continuity mistake: During the Moscow car chase, Bourne hits two barriers that slide through the intersection, one being on its side. In the next shot, the two barriers are gone and the cars at the light change as well.
Continuity mistake: During the car chase in which Bourne gets shot in the shoulder, his hands get covered with blood, but in several shots his hands are perfectly clean.
Continuity mistake: When being pursued by the Russian agent in India, the girl is shot through the rear window of the vehicle. Yet when the vehicle is pulled out of the river, the rear glass is intact.
Continuity mistake: In the main car chase through Berlin, Jason's car is T-boned by the Russian assassin's black Mercedes 4x4. We see a shot of the car spinning and the back bumper/fender is hanging off, held on only by it's very tip on the left hand end and dragging behind. However, in all subsequent shots it's still attached.
Character mistake: When Marie joins Bourne in the bathroom while he's getting medicine, Marie says he's burning up. She gets a washcloth, wets it and dabs Bourne's neck. She only had what couldn't have any more than a tablespoon of water and dabbled it less than a few seconds. It couldn't have had any effect on someone who was burning up.
Continuity mistake: At the start, the first wire put into the right most portion of explosives changes position between shots.
Chosen answer: They frame Bourne because Borne was actually the one who killed Neski and his wife (he was doing it on Conklin's orders). Once Pam Landy does some digging, she will realize this; then it's a simple matter of putting two and two together - the man who killed Neski would obviously have a huge motive for covering up his crime. This is why Abbot and Gretski frame Bourne: he's the perfect fall guy.