Marie tells Bourne that the number for the guy in the bank is 46782255. When Bourne dials the number, the last numbers he is seen dialing are 4321.
As Bourne tries to shoot Carlos at the church, he fires a total of 9 shots out of a 5-shot revolver.(5 shots at the car, then 2 at the guard and than 2 more as he chases the car).
In one scene, Marie St. James mentions an underground tunnel between the terminal building and the parking lot at the Ottawa airport. No such tunnel has ever existed.
When Bourne shoots buckshot at a gas tank from fifty meters/yards, buckshot from that distance would not make a gas tank combust (it probably won't even make a dent), and lead pellets do not spark when they hit cast iron.
When Bourne shoots a man on the steps when he's trying to meet up with D'Anjou, you can see wires leading to his 'bullet wounds'
Obvious stunt double when Bourne crashes the car into a street-car.
In Zürich at the river, Bourne fires a silenced pistol, yet you hear normal gunshots.
When Bourne rescues Marie, he fires what is supposed to be a silenced pistol at the man who was trying to rape her, but the sound is clearly from a gun without a silencer/suppressor.