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.
Visible crew/equipment: During the fight sequence "The Last Two" between the remaining Treadstone agents, after Bourne is first shoved into the venetian blinds, look on the lower right corner (behind the wall) for a camera operator's hands and the lens hood of their respective camera. (00:41:40)
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: The blue Saab convertible belonging to the Berlin-based assassin is parked with all wheels on the road when the call-in team arrives in a silver 4x4. Shortly afterwards, the same car parked almost completely on the sidewalk when the assassin's house explodes. (00:41:50)
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.
Deliberate mistake: When the Neski file exchange takes place in the beginning, the Russian says "You can see who stole the money" and the camera shows the Russian documents. The documents (written in Russian), are in fact, a "Journal of Military Activity of Russian Army in April 1945." It is completely bogus and have nothing to do with the film. (00:07:15)
Visible crew/equipment: At the beginning of the film, the top of a crew member's head is reflected in the mirror of the bathroom cabinet as Jason closes it. (00:02:15)
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.
Factual error: When Bourne's passport is checked at the border leaving Germany to Moscow, his fake Russian last name, Kiniaev, is incorrectly spelled in Cyrillic (Kiniyaev). (01:18:15)
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.
Other mistake: When Bourne's 4x4 is recovered from the river, there is no damage to the rear window. But Marie was shot in the back of the head while driving away, so there should be a bullet hole. (00:20:35)
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.