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)
Continuity mistake: When Bourne is being chased by the assassin, he leans his seat back all the way in order to switch seats with Marie. After they switch, in the next shot of Marie the seat is back up and she has a seatbelt on. There was no time to do either of those, much less both. (00:15:00)BillyBlake
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: 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: When Bourne does in Berlin the online research in the newspapers about the two murders he is accused of, in the first shot (over Bourne's shoulder) the first word in the entry mask of the search engine is "Medienprodukt" (which, by the way, is a verbatim but bad translation of "media product" and no German would say that). Also in the field "Jahr" (= "year"), we can see that the numbers "198" (instead of 199) have been entered. In the next shot, the close-up of the entry mask, "Medienprodukt" has switched to the better translation, "Medium". The entry in the year field has switched to "1997 - 1999". (00:57:35)
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)
Factual error: When Bourne arrives in Moscow at Kievskii station, he goes to check the address of the dead Russian reformer's daughter, looking in a phone booth yellow pages. There are no phone books, much less yellow pages, in Moscow phone booths. (01:21:20)
Revealing mistake: When the demonstration crowd is assembling in the plaza, there's a yellow tram entering on the left hand side. Watch as someone walks across the tracks in front of it and disappears through the corner of the cab. The shot must be a composite of the crowd amassing and the tram shot separately and then overlayed.
Factual error: When Bourne escapes from the Hotel Brecker he comes across "Zoologischer Garten," which is near Kurfürstendamm and therefore fine. But after a little more running he finds himself at the train station "Friedrichstraße," which is four stops away from there. He then jumps off the bridge. Since there is no bridge near Zoologischer Garten, this is probably the reason this mistake was necessary.
Factual error: While supposedly being in Moscow, Bourne really gets chased past the German Foreign Ministry. This is a landmark building. A picture of the building, same perspective as in the movie, is found here: http://www.stadtentwicklung.berlin.de/pix/baubilanz/regierungsgebaeude/auswaertiges_amt.jpg
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.