When the assassins are coming up after Bourne has talked to his boss you see the third assassin inserting a new magazine into his rifle. However, the sound heard as he inserts the magazine is that of a round being chambered. Additionally, right before he is shot by Bourne as Bourne falls, he is heard to chamber another round (this would in actuality be correct at that point, as he hadn't chambered a round initially, only loaded a magazine.)
After the assassin breaks through the window into Jason's apartment, he empties his submachine gun in three bursts. When the magazine is empty, you can hear "click click click click click click click". In reality, when the weapon is out of ammunition, there would be one click only as the weapon is a Micro Galil and fires from a closed bolt with no bolt hold-open device.
When Bourne and Marie are about to abandon her car in the garage, Bourne says he'll wipe down the car (of fingerprints) but by then it is clear that it is known who they are so wiping the car clean would be a waste of time, something Bourne would know.
The two police officers who wake up Jason on the park bench in Zurich speak standard German with a strong Swiss German accent. They would have talked to Jason in Swiss German before perhaps switching to German once they realized that he was not Swiss.
When Jason is telling Marie about his situation in the cafe on the highway, the red bag is on Jason's right next to the aisle. In mid-sentence the camera switches to a long shot and the bag has jumped to Jason's left and is flush against the wall. When the camera moves back, the bag is back to its original place.
Close-ups of Marie holding the papers from the assassin's bag (when she examines the contents of the bag at the apartment and then in the car at the train station), the nails on the hands are long with clear polish, but Marie's nails are short with multi-colored dark polish.
When Jason opens the safety deposit box in the Gemeinschaft Bank in Zurich, the contents are spread evenly around the tray, with the heavy gun on the left. But the box had just been carried upright (by the handle) and set down on the table, so that the contents should all be in a heap on the right-hand side.
When Bourne steps onto the hand railing of the fire escape, the railing is swinging loosely and is clearly not attached to the wall of the bank. Then there is a close-up shot of the railing breaking loose from the wall.
When Bourne is on the fire escape at the consulate and he drops the red bag, there is a car parked beside the building. In the next shot, we only see the bag. The car has vanished. Then as he swings onto the ledge, the car is back. Then as he climbs down the wall, the car has disappeared.
When Jason is climbing down the wall at the consulate, he starts to move around the corner to his right and the lamp is below him. But in the next shot, as he is finishing the same move, the lamp is beside him.
When Jason finds the hidden items in the safety deposit box there are two green passports on top with the top one being from Brazil. At this time his hands are empty. He is then shown reacting to a noise and turning around with a green passport in his hands. When he reaches back into the box, the passports are still in the same order.
At the consulate, while Jason ascends the stairs, there is a shot in which feet are visible at the top of the final flight of stairs. The next shot shows Jason from the front, and there is no one around.
The BMW used by The Professor can be seen earlier in the film, used as an "extra" during the car chase through Paris. During the same chase, another car, a BMW 735 is seen parked and unoccupied during the same chase when a couple of pedestrians leap onto the bonnet to avoid Bourne and Marie in the Mini; 30 seconds later, this same car is seen driving along the side of the Seine prior to being involved in an accident with a police motorcyclist and another vehicle, sustaining substantial damage. Just over a minute later, the same car is seen, undamaged, braking to let Bourne and a police car out of a side street.
After Jason shoots the gas tank, the Professor's view of the farm is obstructed by thick black smoke. When we see the tank from Jason's point of view, the smoke is white, relatively sparse and can easily be seen through.
While Jason is clinging on the side of the consulate wall under the catwalk, he looks down at the bag on the sidewalk after the Marines close the door. When we see the bag from Jason's point of view, we can see the catwalk railing in the bottom of the shot indicating the camera is standing on the catwalk and not from the wall below it.
In the consulate, we first see a Marine Corps SSgt handing out weapons from the armory to the Marine security force before pursuing Bourne. When we next see him he is equipped with a Heckler & Koch MP5K submachine gun. When the same SSgt then opens the catwalk door to look around for Bourne, he is shown carrying a Colt M-16 rifle.
When Jason finds his passport in the safety deposit box, it shows his address in French postal code 75005. When he catches the assassin in his house, they find instructions telling the assassin where to find Jason's house, and the sheet lists his house in French postal code 75006.
When sitting in the car outside the train station we see someone walk to the right in the background pulling a blue suitcase wearing blue jeans and a khaki top. When we cut back to the same view a few seconds later the same man is walking past again to the right.
Conklin removes his coat on the Pont Neuf as a signal for Jason to call. In the close-up, he removes his raincoat, but his suit jacket is still on underneath. However, in the long shot, both coats are removed exposing his dress shirt.
During the close quarter fight at the consulate, the cap falls from the Marine's head three times: when Jason twists and locks his arm, when he parries his baton and finally when Jason pushes him back.
When Jason is talking to Marie in the car about giving herself up to cops, some cops approach the car. In the following chase scene Jason backs up his Mini and nearly hits the front part of the bus. Then a police cars takes the place between his Mini and the bus. In the following shot however you can see absolutely no cars or buses behind the cop. After this the bus is on its place again.
At the consulate sequence in Zürich, when Jason escapes via the fire escape platform by going under it and clinging to the side of the building, he basically clears most of the previously undisturbed snow off the platform. However, when the marine arrives moments later, the platform is again covered with undisturbed snow as it was before Jason arrived at the platform.
When the professor is driving the BMW at night, the only lit exterior lamps are the daytime running lamps (high beam bulbs running on low voltage). However, when we see the interior of the vehicle in the next shot, the orange dashboard lights are illuminated, which would only occur if the car's parking or headlamps were turned fully on.
When Marie is about to leave the farmhouse with Eamon, the waiting red vehicle has both doors open on the right side. However, when she finally decides to get in, only the back right door is open for her. The front door is closed.
At the beginning of the mini car chase, just after Jason performs a J-turn and speeds off down the road, he brakes for the corner and his left brake light is out. In all subsequent shots both brake lights work.
The windscreen of the Mini is cracked after crashing into the glass door of the telephone booth during the car chase. When Jason and Marie park the Mini, and when the police discover it, the windscreen is not cracked.
When Jason parks the Mini in the underground car park, there's a wall to the right of the car. A few scenes later when the police find the car, there's a covered car to the right of the mini and no wall in sight.
When Jason is first loaded on the fishing boat in the beginning of the movie, and later when he is shown on Wambosi's boat and in the ocean after being shot, he is wearing a wetsuit. However, several scenes show Jason wearing a knit sweater with bullet holes in the back matching wear he was shot. He was not wearing that sweatshirt when he was shot, nor would it be practical to be diving wearing it.
After Marie calls Eamon's house from the parking lot near the highway, she crosses the lot to where Jason is taping up the rear passenger window. During alternating shots, the car is in the same position until the last shot where it is now parked on the other side of the lot (closer to the pay phone).
When Jason is going to collect his safety deposit box he has to put his hand on the screen for it to recognize his fingerprints. The machine turns green and Jason takes his hand from the screen, yet in the next shot, he takes it off the screen again.
When Jason is hanging from the fire escape at the consulate he looks down to see where to put his feet on the narrow ledge. There are already two shoe prints in the snow right where he places his feet.
While recovering on the fishing boat and in the Zurich scenes, Bourne is wearing a sweater with holes on the back that match the locations of his bullet wounds. But when the boat captain cut the wet suit off to administer first aid, Bourne was not wearing a sweater beneath it.
When Jason and Marie are driving from Zurich to Paris, they can be seen on a country road next to a railroad track with high mountains in the background. While it is true that between Zurich and Basel, the railroad track is at some points next to the road, they would certainly not have taken a country road. There are highways directly leading from Zurich via Basel to Paris. Furthermore, there are no mountains that high anywhere near the route they are taking. The only mountains that could possibly be seen by them is the Jura, which is no higher than 1720 meters. The mountains shown are however clearly supposed to be the Alps.
The tram in Zurich which nearly hit Jason is correctly labeled with signs from the Zurich tram line 10. But the vehicle itself is definitely not from Zurich. It has also the wrong track width (Zurich has a track width of 1000 mm). Filmed in Prague.
When Jason and Maria drive from the US consulate in Zurich (filmed in Prague), through the side window a large concentration of cheap and old Eastern European cars (including GDR's plastic vehicle Trabant) can be seen parked by the pavement. Possible in Prague, impossible in Zurich.
The names on his Russian passport are written both in Cyrillic and Latin letters. In Cyrillic they say "Lshtshfum, Ashef" (which is a total nonsense - it is matching Russian letters from buttons on English keyboard), and in Latin letters it is "Kiniaev, Foma". (In the sequel The Bourne Supremacy, his Russian passport correctly has "Kiniaev, Foma" in both scripts.)
One of the musical score songs is entitled 'On Bridge No. 9', referring to Bourne and Conklin on Pont Neuf in Paris. While 'neuf' is 'nine' in French, it is also the masculine singular for 'new', which is the case here. Pont Neuf is actually the 'New Bridge' in Paris, not 'Bridge No. 9".
Bourne arranges to meet his boss on the bridge at 5:30pm. From the farmhouse decorations we know it's around Christmas time. At 5:30pm in Paris in mid-winter it would be almost, if not completely, dark.
When the Professor is shooting at Bourne at the farmhouse, his first shots are on full auto, clearly audible. But the selector is set to single fire and the auto lock is on, seen in a sideways shot (the white circle behind the selector). You need to open the rifle up to unlock the auto switch, otherwise the selector is locked to safe or single.
When Jason is briefing Marie, before she goes into the hotel lobby, he asks her what the number for the payphone is. She responds, "616-2468" (a 7 digit number). In Paris, pay phones and fixed phones have number 01XXXXXXXX (10 digits), usually given in pairs.
While the license plate on Marie Kreutz's Mini Cooper shows basically the correct design ("ZH" as acronym for Zurich and the Swiss cross), the typeface of the letters and of the figure is not as on official license plates in Switzerland. And there would also be a small black dot between "ZH" and the figure, which is missing in the movie.
When Bourne is checking his Brazilian passport, the name Gilberto de Piento is not his, but the consul who issued the passport. In the old version of the Brazilian passport, like the one he owns, the personal information would be on a separate page from the photo.
At the beginning of the movie, when the Italian sailors drop Jason off, we see him walking away on the port. A car passes by, and he apparently vanishes. You can see him running behind it, and his feet show on the reflection beneath it.
When Treadstone activates its assassins, and the Professor is shown teaching how to play piano, he checks his phone, and the message text is shaking as he closes the phone, indicating that the text originally was not displayed by the phone, but it was digitally added later.
When the assassins receive their messages on their cell phones the first one receives the message on a Motorola phone which - as other phones also - isn't able to display the short message in the way as shown with light letters in small dark bars. The message clearly looks like a computer overlay.
When Marie and Jason are driving to Paris it is obviously in the dead of winter. When they arrive in Paris and Marie awakens Jason to give him breakfast, the trees in the background are leafed out and are completely green. The morning arrival scene in Paris was obviously filmed at an entirely different time of year. The subsequent scene of Marie and Jason driving to Jason's apartment shows the trees bare again.
The goof items below may give away important plot points.
When Wombosi is shot through the window, glass is clearly breaking out from the lower part of the window. When we see through the Professor's scope the bullet holes are at the upper part of the window.
Right before Wombosi gets shot, he is coming down the stairs wearing a turtle neck and carrying a jacket in his left hand. The instant he gets shot, he is wearing the jacket, and falls down the stairs with it on.
From the first viewing of Eamon's farmhouse through The Professor's rifle's viewfinder until the time that Eamon, his children, and Marie drive away, the red Jeep Cherokee alternates between pointing in towards the property (as when Eamon arrived) and pointing away (as when they are leaving). This happens not just once, but twice, although the car would not have been moved by anyone at all while they were sleeping overnight.
(at around 1h 28 mins) In the field behind Eamon's farmhouse, as Bourne shoots the Professor for the second time, a crew member can be seen running through the trees on the hill over Bourne's right shoulder.
At the end the camera pans across a Mediterranean vista to a plaza where Marie now lives and works. We hear what is usually regarded as the dolphin call. The sound has long been known to be the doctored call of an Australian kookaburra bird, but since the days of Flipper has been Hollywood's substitute for the sound of a dolphin.
When Ward Abbott is testifying on Capitol Hill about the CIA's programs, there are Washington, DC city flags behind the panel to which Abbott is speaking. Although the event is taking place in Washington, there would never be city flags displayed at a Federal or Congressional proceeding, only USA flags.