Continuity mistake: When Bourne is talking to Firsch, the gun he is holding changes from a Glock in the shots facing Bourne, to a SigPro when the shots face Firsch.
Visible crew/equipment: Many shots when they are in the CIA building, you can see the cameraman in the glass walls.
Continuity mistake: In the chase scene involving Bourne and Desh, when Bourne comes to a stop on the rooftop, his jacket is zipped. In the next shot his jacket is open. In the next shot his jacket is zipped, as he begins to run again.
Continuity mistake: When Landy is looking at Jason's file it says his blood type is A+. When Jason looks at his old dog tags it says his blood type is O-.
Continuity mistake: The conversation Bourne has with Landy at the end of The Bourne Supremacy is repeated in this film, about an hour and fifteen minutes in - the conversation is absolutely word-for-word identical, so clearly it's the same one. However, in Supremacy, it is a bright, sunny day, but in Ultimatum, the weather is overcast with snow on the ground. Landy's phone rings in Supremacy, but vibrates in Ultimatum. Finally, the other agent doesn't enter her office during the phone call in Supremacy.
Continuity mistake: When Desh is chasing Nikki and Bourne is chasing Desh, in a shot of Bourne from overhead, he is wearing black converse type tennis shoes (black with white rubber on the toes). As the chase continues, Bourne's shoes are shown several times to be solid black.
Continuity mistake: When Pamela Landy is looking at Jason Bourne's induction paperwork, the date of his induction is 06-01-1999. However, the date of his first assassination (Neski) is 1998. The assassination of Kyriacou is also listed as having taken place in 1998. Both dates are obviously before he had completed the Treadstone induction. (01:11:55 - 01:13:25)
Other mistake: At the beginning of the New York chase sequence where Bourne is walking down the street, you can see an Asian man smiling right into the camera for a second.
Factual error: When Bourne is traveling to London on the Eurostar from Paris, immediately after the 'flashback' where Marie floats away after being killed, there are two helicopter shots of the Eurostar traveling to London. The second (far away) shot shows the train passing over a motorway. The train is actually traveling towards Paris, and therefore away from London. The motorway is the M20 and the bridge is approximately 3 miles west of junction 9 for Ashford (Kent). The train would have been 10 minutes away from entering the Channel Tunnel. (00:13:45)
Factual error: When Jason is at the internet cafe googling the financial company, the address that comes up for Sydney is not technically possible. The street name (Market Street) is real, but the street number was 18017 which is not possible as the street is only a few blocks long and ends at about 400. (00:29:00)
Continuity mistake: When Bourne is fighting with Desh in the bathroom scene, the wash basin gets broken off the wall.But in the next camera angle it is back in place again.
Continuity mistake: When Nicky is first seen in the movie, with Bourne pointing a gun at her, her hair changes between shots.
Continuity mistake: At the end of the movie, in the flashback when Bourne recalls his training process several years ago, Hirsch looks younger, but Bourne looks just like the present date, with an edgy and thin face, opposite to the round-childish face that he had then (which we are reminded of during all the movie via photos in his portfolio).
Factual error: When Jason is in the Internet Cafe in London he Googles for Sewell and Marbury, when he gets the results he doesn't have "The "AND" operator is unnecessary - we include all search terms by default. [details]" which should have been displayed just below the search box. (00:28:55)
Plot hole: Landy uses the code 4/15/71 to point Bourne to the training site address. But how does he know it is on the East side?
Factual error: When the first assassin drives to Waterloo station to take out Simon Ross and Bourne, he is driving a BMW 3 series with a 2006 UK licence plate. However the events in this film are meant to follow on six weeks after the previous film, which make it still set in 2004.