Continuity mistake: When Bourne steals the police motorcycle the rear left emergency lights are broken and dangle down to the left. In a following clip, the broken light is on the right. It appears they mirrored the footage.
Factual error: When Bourne goes to Berlin, he supposedly heads for Kollwitzplatz. There is even a street sign in the shot to reinforce that connection. Problem is that Kollwitzplatz is in Prenzlauer Berg and Bourse is actually heading down Falckensteinstrasse. You can see the Oberbaumbrücke in the background. Presumably, Kollwitzplatz, as a famous iconic location seemed like a better choice. If you compare it to google street view, you can see how they changed the traffic signs. (00:43:47)
Character mistake: During the Athens scene, Dewey says "It's David Bourne. Clear to engage the target" mixing up David Webb and Jason Bourne's names. (00:00:22)
Suggested correction: He says "Stay with Bourne." The two had split up and he wanted Jason followed.
Other mistake: The asset is speaking on his cellphone, but he's holding it upside down - you can see the camera. (01:21:54)