In London we clearly see a car with a license plate beginning LT56 indicating that the vehicle was first registered between September 2006 and February 2007 - after the time in which the film is supposed to take place.
As Jason looks over the paper while riding the train near the beginning of the movie, we see the story he is reading. It reads, in part, "His code name was Jason Bourne, but he had many identities, each one seemingly more deadly then the next." This is a case of then/than confusion... it should read "than the next". It should however be noted that the newspaper in question, "The Guardian", used to be notorious in the UK (in the days of manual typesetting) for its spelling mistakes, leading to its nickname of "The Grauniad". It is just conceivable that this is a nod to this reputation.
Character "Neal Daniels" has his first name spelled both accepted ways: Neal and Neil. In the scenes where he's being tracked on the computer it's Neal; later, while Pam flips through some CIA papers, it's Neil.
Most fax machines scan before sending. All Vosen has to do is press cancel and the fax would not be sent. In fact, as he enters the room the fax can be heard to make the first beep of the sending tone, indicating that it's only just beginning to try and send the fax. However, being a high-up member of management in his 50s or so, it is entirely possible that Vosen has no idea how to work a fax machine and so might think it had already sent. Also, this model of fax machine scans with the pages facing down, so he would not see what was scanned until the pages came out. Since they were put in face-up Landy would be scanning blank paper (if there was nothing on the back).
In the last and most spectacular window-to-window jump scene in Tangier, Bourne is holding a gun in his right hand when he jumps off. The immediately following in-air shot from below shows him with the gun in the right hand still, but the next in-air shot from behind shows him with no gun in the right hand while his left hand is covered by his body. When Bourne crash-lands, neither his hand is holding the gun any more, but then he stands up to fight Desh, and the gun suddenly returns into his right hand. This is explained on the extras on the DVD. The shot of the jump was flipped vertically by the editing team.
When Nicky Parsons is on her laptop trying to locate Neal Daniels, and is logged on to her CIA account, when the camera shows a side view of her typing, her screen does not show the CIA screen but the Desktop, it then switches back to the CIA screen in the next shot.
When Jason is across the street in New York watching Vosen and Landy, Vosen places the Blackbriar casebook in his briefcase twice. First he places it in when we see him from Jason's view, and again right after when we see the close up (through the binocular).
When Jason Bourne hot-wires the Audi on the parking garage rooftop, he puts it in drive and slams into a parked SUV pushing it forward. He then puts it in reverse to escape other agents. As the camera shows the full screen shot of the Audi, the front of the car is completely undamaged - like new.
At the end of The Bourne Supremacy, when Jason is talking on the phone with Pamela Landy (and subsequently walking through the streets of New York), it is clearly summer time, with the trees in full bloom and people in short-sleeve shirts. During the middle of The Bourne Ultimatum (when this scene is re-shot as a significant part of Ultimatum's plot structure), it is now suddenly winter, with Pamela Landy having to wear a heavy coat, gloves, and a scarf outside, and there is clearly snow on the ground.
In the Waterloo scene, right before Jason tells Simon Ross to tie his shoe, Ross's bag can be seen over his left shoulder. When he kneels down to "tie his shoe," his bag is over his right shoulder. When he gets up again, the bag is again over his left shoulder.
In the Waterloo scene, Bourne walks from right to left but an upshot shows a camera rotating left to right, obviously missing him. However, on the next shot we can see on a monitor an image of Bourne buying a cell phone from a shop.
As Pamela Landy is reviewing Jason Bourne's Treadstone file, we see a report on Bourne's assassination of Vladimir Neski in Berlin. In The Bourne Supremacy, Nicky Parsons insists that Bourne never worked for Treadstone in Berlin and that the Neski job is "not in your file;" thus it should not exist for Landy to read.
After the explosion scene that takes place in Tangier, Jason gets up and walks down a slope to chase Desh. While a subsequent shot shows Jason wearing a pair of dark shoes, in a shot that follows immediately, the shoes he wears magically turn into a pair of white-color sports ones. But in next shots, the shoes become all dark again just as they always are.
In the scene where Bourne calls Landy, which also is the final scene of The Bourne Supremacy, Landy's cellphone vibrates and she picks it up. However, in The Bourne Supremacy, Landy's phone rings, it does not vibrate.
In the flashback, Bourne's final test is to execute an anonymous captive. He uses the Mozambique technique (body armor drill, to those in law enforcement)- two shots to the body, one to the head. However, when the captive's hood is removed, there is no evidence of the head shot.
At Waterloo when Paz is lining up a shot on Simon Ross through the advertisement board, one shot clearly shows the time in digital format being '12.50'. However, when Neal Naniels is in the safe house station later that day, the news reporter claims that he was shot at around '15.45'.
In the explosion scene in Tangier, in a shot aimed uphill, Desh appears between the two rows of cars; in the downhill shot he's gone, and then he reappears in the next uphill shot. (Yet he clearly hasn't moved.)
In the first scene the location is identified as "Moscow, Russia" and Jason Bourne is chased over a bridge crossing railway tracks and into a station identified as "Kievsky Station". The station is in fact Berlin-Lichtenberg.
The Sydney address for Sewell & Marbury is given as 18077 Market Street, Sydney 20031, New South Wales. Tel: 582 9232 2360. Australian street numbers start at 1 and go as high as the length of the street - the highest number in Market Street is 120. Australian post codes are 4 digits - the correct post code is 2000, or 2001 for a general post office address. Australian phone area codes are two digits - the correct area code within the country is 02. The country phone code for Australia is 61 - if the phone number is supposed to include the country code, then it should be 612. However the phone number is in the correct format for Sydney's CBD.
At the end of the movie when Jason jumps off the roof , he would have to make a very super jump to land in the east river. 451 E. 71st is over a 1/10th of a mile from the east river. It is located at the corners of E.71st and York ave.
When Bourne is checking Daniels' Madrid office, the calendar, in Spanish, reads January 10. The montage cuts to the CIA office in New York where the Empire State Building top is lit all in green. These colors are reserved for holidays such as St. Patrick's day. The color scheme for January 10 is all white lights.
At Waterloo Station in London you hear Bourne instruct Simon Ross to go to the bus stop and stand near the man with the hooded top. The approaching bus is a No.43 that runs from Friern Barnet to London Bridge - this bus goes nowhere near Waterloo Station.
When Bourne follows Desh on the scooters in Tangier, Desh receives a phone call. He handles the cell phone with his right hand which controls the throttle on the scooter. By taking his right hand off the throttle, the scooter would suddenly have slowed down.
When the Spanish police stop the American CIA operatives in the street as Jason and Nicki leave the Madrid training facility, the police are heard yelling "Hande Hoch" ("hands up") in German, not in Spanish or English.
The Chevrolet Impala police car driven by Jason Bourne executes sudden slides and, on several occasions, is shown to "lock" the front or rear brakes and wheels. All Impala police vehicles are equipped with anti-lock brakes, which would make this behavior impossible.
At Waterloo Station, as Bourne is preparing to drop the phone into the Reporter's pocket, two extras are walking towards the camera - a man with a beret (on the right) and a woman with a white knit hat (on the left). In the next shot of the reporter, the same two extras walk around the corner, except they've switched sides
As Jason is reading The Guardian on the Eurostar train, the text of story he's reading contains a double dash ("--"). This form of punctuation is not used in British typesetting, the spaced en dash (" - ") being preferred.
When the reporter is shot at Waterloo station, during the through-the-scope footage, his head never actually make it to the crosshairs. His head approaches them but then whips back from the bullet impact before ever being framed by the crosshairs.
(at around 36 mins) Bourne looks at the monitor of the security camera that displays a car approaching the compound. The camera seems to follow the car, and even zoom in and out to maintain a good composition - not the sort of shot expected expected from a security camera.
The goof items below may give away important plot points.
Bourne is first given his dog tags while holding a gun in his right hand. When he turns one of the tags over with his right hand to read his real name, his hand is empty. The gun is back in hand in the next shot.
Similar to Jason's disappearing cuts and bruises, the "asset" in the NYC car crash appears bloodied and bruised in the car, but when confronting Jason not more than an hour or so later he appears without any cuts, bruises, or even dried blood. After getting brutally punched and elbowed in the face by Desh, Nicky Parsons has no signs of bruising or other damage just a few hours later.
As Pamela Landy is reviewing Jason/David's file at her desk, David's blood type appears to be A Positive. On the dog tags that Jason is handed back in the training facility, David Webb's blood type is O Negative.
On the news report following the shooting of Simon Ross, it is announced that he was shot at 3.45, yet in the scenes leading up to this in Waterloo station, the announcer can clearly be heard calling out trains leaving at 17.45 onwards.
The type of pistol Bourne holds against Dr. Hirsch's head near the end of the movie changes. In shots over Bourne's shoulder prior to the complete flashback (showing Dr. Hirsch) the pistol is a Glock. In shots over Hirsch's shoulder (showing Bourne) the pistol is a Sig Pro, as revealed in Vosen's office. Following the complete flashback, the pistol is a Sig Pro both in shots showing Bourne and in the reverse.
When Landy is reviewing Jason's dossier, lines that seem to be on the top of the page in one shot are shown to be in the middle of the page on a subsequent shot. In addition, the lines describing Dr. Hirsch's contribution to Jason's indoctrination are first seen as a paragraph on the chronological record, then as a paragraph to the right of Dr. Hirsch's picture on what looks like a résumé.
While weaving in and out of traffic during the car chase through New York, Bourne's police car is sideswiped by agents chasing him, has several other multiple collisions, then goes through an intersection with the car having been substantially damaged on all four sides. It flashes to the next scene with the NYPD car shiny, new, unscratched and without a dent. At other points in the chase, the rear bumper changes position after it has been substantially damaged. In one shot, the bumper is dented but still intact. In another shot, the bumper is hanging off the back of the car. This change happens several times.
In the scene at Waterloo station after the reporter is shot we see police officers rushing to the scene with the sound of whistles blaring... UK police do not use whistles to attract assistance instead relying on a radio system. Later outside we also hear the traditional 'two-tone' siren as more police arrive, again US style wail/yelp sirens are the norm and have been for over a decade now.