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.
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.
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.
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.
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).
Continuity mistake: When Desh goes to meet Nicki, he parks his scooter. Walking behind him(from left to right) is a guy wearing a black shirt with orange stripes. The camera then switches to Bourne and then back to Desh. The man in the shirt is now seen walking towards Desh(from the left) but is still at least 40 feet away from him.