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
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
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: 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?
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 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.
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.