- Continuity: The cuts on Jason, especially over the left eye, appear and disappear following the police car crash.
- Continuity: 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.
- Continuity: 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.
- Errors made by characters (possibly deliberate errors by the filmmakers): 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.
- Continuity: 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).
- Factual errors: In the Port Authority Bus Terminal garage, Bourne is confronted by an NYPD car. The Port Authority has its own police force, so it should have been a PAPD car.
- Continuity: 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.
- Continuity: In Nicky Parsons' first scene, confronting Bourne, the right side of her bangs change positions in every shot from over her eye, behind her ear and just hanging freely.
- Continuity: In the chase scene where Jason Bourne is in the police cruiser, his 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.
- Errors made by characters (possibly deliberate errors by the filmmakers): 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.
- Factual errors: When Bourne types the bank name in the google-bar, the CAPS-lock function of the computer is still on, but lowercase letters appear on the screen
- Revealing mistakes: When running around a busy corner in the streets of Tangier, a bystander can be seen taking a photo of Nicky Parsons (Julia Stiles) with his cell phone.
- Revealing mistakes: 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.
- Continuity: When Bourne returns to NYC, there is an aerial shot of two ballfields with perfectly green grass, and no snow. Yet in several places on the streets, there is plenty of snow.
- Factual errors: In the Moscow militia chasing scene, the letters DPS (in Russian) can be seen on a big van. DPS means "highway patrol". They wouldn't be chasing a foreigner on a train station. Train stations throughout Russia have their own militia.
- Factual errors: In the Moscow militia chasing scene, Bourne breaks into a pharmacy. Russian pharmacies are guarded at night by armed guard. It's a law provision.
- Continuity: As Bourne is driving out of the parking garage in the police car, the car's headlights are on then off then on again in successive shots.
- Factual errors: When Jason is looking for "Sewell & Marbury", the Madrid address shows "334 Calle Norte". In Spain (and the rest of Europe) they would have written "Calle Norte 334".
- Continuity: When Bourne goes into the training facility, it is light outside. He is told he has 3 minutes before security arrives. After he is done in the facility and jumps into the river, it is night (not even dusk).
- Errors made by characters (possibly deliberate errors by the filmmakers): Most fax machines scan before sending. All Vosen had to do was punch 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 was 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.
- Revealing mistakes: 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
- Errors in geography: 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.
- Miscellaneous: Stuntman 'Dominic Preece (I)' is credited twice in the credits.
- Revealing mistakes: When Bourne shoots the guy on the chair in the hard surface Training Center room no-one is wearing ear defenders and no-one flinches at the reports.
- Factual errors: In the scene where Bourne drives the car off of the roof, he hot wires the vehicle which would be impossible without using equipment to bypass the factory security first. Otherwise the vehicle's fuel pump would be disabled.
- Continuity: When Landy checks Bourne's file his blood type is listed as A positive. When Hirsch hands Bourne his dog tags from when he changed his identity his blood type is listed as O negative.
- Factual errors: Strict U.S. government rules on the handling of classified material prohibit viewing such documents near windows, where unauthorized individuals (like Bourne, from across the street with a telescope) can see inside and read them.
- Continuity: In the Police Car Chase, the Volkswagen Toureg SUV is seen smashing frequently into the police car. in a few different scenes the Toureg is seen with a damaged front end, and in later scenes, it's seen with a more/less damaged front end.
- Continuity: In the fight between Bourne and Desh the sink in the bathroom becomes dislodged from the wall. At the very end of the scene the sink has miraculously been reattached.
- Continuity: 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.
- Revealing mistakes: When Pamela Landy is examining the file of Vladimir Neski his name is written as "Vlademir" when it should be "Vladimir".
- Continuity: 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.
- Factual errors: 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.
- Errors in geography: 415 E 71st St. is not on the East River. It's actually a walkup apartment building between 1st and York Avenues. Moreover, Bourne jumps from the roof of 415 E. 71st St. into the East River. This could not possible as that building is between First and York Avenues, more than a full city block from the river.
- Continuity: The movie does not explain why Jason Bourne travels from Paris to London in the first place. He only reads the article of Simon Ross on Treadstone and himself on the Eurotrain, having just bought the newspaper at the Gare du Nord before boarding the train. On the DVD, a cut scene from Paris reveals that he is directed to London and Ross by an arm's dealer, apparently an old contact from Treadstone days.
- Continuity: When Bourne arrives in New York, and is paged as a message from Pam Landry, the page is for a Mr. Gilberto de Piento. If you look at The Bourne Identity, when he retrieves the passports from the bank deposit box, Gilberto de Piento is the Consul General who signed the passport, not his name on the passport. His name on the passport is Joao do Carmo.
- Continuity: Wrong gun used in one shot. When Bourne is confronting Dr. Hirsch toward the end of the movie, the handgun he threatens the doctor with changes between shots. Initially, he holds a covered-hammer design pistol (possibly a Glock) to the doctor's forehead, but later the weapon is replaced with what appears to be a Sig Sauer P229 (an open hammer design). The gun used in the flashback sequence depicting his original induction into Treadstone is the Glock.
- Errors in geography: 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.
- Continuity: In the newspaper article showing Marie's photo and marking her death, her name is Victoria Marie Kreutz. In The Bourne Identity, the original Treadstone crew identifies her as Marie Helena Kreutz during her initial introduction.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: SPOILER: 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.
- Continuity: SPOILER: 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.
- Continuity: SPOILER: 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.
- Continuity: SPOILER: 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.
- Continuity: SPOILER: When Jason has returned to NYC, he is once again escaping, this time in a stolen NYPD car. As he weaves in and out of traffic, is side-swiped by agents chasing him, has multiple other collisions, and then goes through an intersection with the car having been substantially crashed on all four sides. It flashes to the next scene with the NYPD car shiny, new, unscratched and without a dent.
- Continuity: SPOILER: 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.
- Factual errors: SPOILER: 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.
- Continuity: SPOILER: 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.
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