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.
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.