In the Moscow car chase, Bourne's car is hit from the driver's side by a police car. The driver's side window breaks. In the next few shots, you do not see any broken glass on Bourne. In the very next shot the car is not damaged on the driver's side.
After Jason steals the car with the tool that he pushes in the
ignition he gets out of the vehicle. When he returns to the car he starts the vehicle. The distinct sound of keys rattling can be heard. So obviously he mysteriously got keys to the vehicle he had stolen. This is because an alternative scene was shot where he approaches the owner of the car and buys it on the spot.
At the beginning of Russian militia sequence in front of the airport we hear radio transmission in Russian. Translation: "This is number 17, I am sorry I could not get there, I got stuck in a traffic jam." Ten minutes later during the cab chase the exact same message is aired again, unrelated to the chase.
In the opening minutes of the film, Bourne has his nightmare in Goa and goes to the bathroom. We hear the fluorescent lamp ballast (choke) buzzing at 60Hz, however if Bourne is in Goa, India like the film says then it should be buzzing at 50Hz.
When Bourne calls Berlin hotels to find out in which one the female CIA executive is staying, he mispronounces "sprechen". This happens several times. A CIA covert agent trained for work in Europe would not mispronounce such a common word.
When speaking in Russian, both Kirill and Bourne make some language mistakes. Kirill, after the operation in Berlin, says "I'll take a shower" like that: "Ya voz'mu dush", whereas the correct expression is "Ya primu dush". In Moscow shop, Bourne shouts "Vniz!" meaning "Down!", and correct expression for that is "Na pol!", or "On the floor!" And when Bourne tells Irina Neski that he won't hurt her he adds "Ponial?" or "understand?" when he should have used the feminine form "poniala?"
When Landy calls Nevins in Naples after Bourne has escaped, she says "I want you to secure that area." But when Bourne plays back the conversation on his tape recorder, Landy is saying "I want that area secured."
When Jason is on the rooftop observing Pamela and staff through his rifle scope, Jason's view of the personnel inside is clear and totally unobstructed. However, camera shots inside the building show sheer white curtains across all the windows.
During the car chase seen in the Moscow tunnel between the yellow taxi and the Mercedes SUV, the Mercedes is shown to have a dangling front license plate. In subsequent shots, the license plate is firmly attached and not dangling.
The taxi gets hit by the Mercedes SUV sideways, spins out, loses its rear bumper and its trunk opens. Yet, when seen from inside the taxi, the Mercedes clearly misses the taxi, and in subsequent shots the taxis' bumper is intact and the trunk is closed.
When Bourne is threatening Abbott he is clearly holding a pistol in his right hand (which he presses against Abbott's neck) while using his left hand to grasp Abbott's shirt collar. A few seconds later, with no way of switching, he is now holding the voice recorder in his right hand and uses his left hand to slam the pistol onto the table beside Abbott.
The clerk at the reception of the Hotel Brecker addresses Bourne in English at once, although she can't instantly know that he is American. In the previous scenes Bourne addressed each person who answered the telephone in German and they answered in German, however in this scene he clearly states "Pamela Landy, please". From this, the operator is likely to have instantly determined the conversation would be in English.
During the fight in the German apartment with Jason's former colleague, Jason clearly has a cut and swollen lip. In the restroom where he washes blood off his hands and looks in the mirror, his face shows no sign of the wounds from the fight.
The last car hit in the tunnel chase scene is a black VW Polo. The following shot, from behind, is actually an earlier scene. The car we see hitting the wall is not the Polo but the first one hit in the tunnel, and Bourne's taxi is not next to the Mercedes but behind it.
During the car chase, when Bourne's taxi enters the main stream of traffic and spins you can clearly see the exhaust pipe broken and hanging down. As the car races away it sounds normal and a couple of scenes later it has magically repaired itself.
When Bourne and Marie switch seats when being chased by Kirill in Goa, Bourne lowers the backrest of the seat and they switch. In shots immediately after, the backrest is shown in the upright position.
When we see Nicky walking down the stairs in Amsterdam, you see a newspaper shelf in the background with the name L'echo. L'echo a Walloonian (Franco-Belgian) news agency and not a Nederlands Dutch one.
When Pamela Landy arrives in Berlin she and her team get into two black vehicles. The next shot shows these vehicles driving down the road and it is clearly visible that the first vehicle's number plate is 'BAS7227' and the second vehicle's number plate is 'BWB942'. However when the shot changes you are able to see the vehicles from the back, and vehicle 'BAS7227' is now second in the convoy while vehicle 'BWB942' is first.
When Bourne uses the yellow taxi in the Moscow tunnel to ram the Mercedes SUV into the lane divider, the SUV ends up at about a 45 degree angle to tunnel wall. But when Bourne get out of the taxi and approaches the SUV, the SUV is shown parallel to the wall.
At the end of the scene where Jason Bourne is targeting Pamela Landy with the sniper rifle, Ward Abbott is standing next to Landy when they all realize Bourne is watching them from outside their window. The scene then rapidly shifts perspective multiple times and in one of those shifts, we quickly see Ward Abbott completely on the other side of the room now standing behind Danny Zorn.
In the 2nd shot shown of the tram is arriving at Alexanderplatz Station, the protestors in front of the tram's path do not move out of the way. One protestor even seems to lose her legs and at least one protestor seems to be 'hit' by the tram so this is obviously a superimposed crowd. You can see the repeat as the white banner and brown banner are duplicated along the tram lines.
When Bourne tells Nicky to enter the tram it is directed towards "Alexanderplatz". The luminous display inside the tram however reveals "S+U Lichtenberg/DB" as destination - a completely different quarter of Berlin that is not connected to Alexanderplatz via tram.
When Bourne discovers and writes down Landy's phone number it has the area code 757. "Langley" (CIA Headquarters) is in Mclean, Va whose area code is 703. Area code 757 is in southeast Virginia, home to Langley Air Force Base.
During the car chase at the end of the movie the location of the chase switches between the road (Naberezhnaya Tarasa Shevcenko) next to the Hotel Ukraine which is opposite the parliament building to a different road (Sofijskaya Naberezhnaya) which is across the river opposite to the Kremlin and then switches back again to the Hotel Ukraine location.
The bank statement in the amount of $760,000 can be seen, where it is depicted like this: "+ 760.000,00", which is the number format that is used in Germany. Since the bank is located in Zurich, Switzerland the format they would have used is "+ 760'000.00".
When Jason enters the train to Moscow at Berlin Ostbahnhof, there is an announcement for a train heard on the platform: "... nach Hamburg. Über Hannover, Bielefeld, Dortmund." (... to Hamburg via Hannover, Bielefeld, Dortmund). There are no direct trains from Berlin to Hamburg going through these towns. In fact, there are not even on the way. Going from Berlin straight westward to Cologne you would get through these cities, Hamburg is farther north and there is a direct connection without any stops (takes 1,5 hours).
After Bourne leaves the Hotel Brecker, he enters the station "Zoologischer Garten", which is actually next to the supposed address of the hotel. After passing through the hall he leaves the building and we see a bridge over a river. "Zoologischer Garten" isn't near a river - the rest of the scene is shot at station "Friedrichstrasse", 4 train stops away.
The water heater that Jason supposedly disconnects the gas line, is actually an electric hot water heater (no chimney). Jason disconnects the hot water line. Also you can't loosen a pipe fitting with out a wrench.
In India, Bourne buys a bottle of water from a street vendor. The bottle is Himalayan Natural Mineral Water, stocked only by upper-class areas of India such as 5-star hotels, embassies and expensive restaurants, not by small street vendors.
An agent scans the planted fingerprint using an HP iPaq PDA. Ironically, although this model does have a biometric fingerprint scanner, he doesn't use it - instead, he lays the fingerprint across the touch screen.
When the militia who stop Kirill check his ID it can be seen that the militia holding Kirills ID maintains his finger on the trigger at all-time. A police officer trained to handle a firearm would be trained to holster it whenever combat was over straight away and have his finger off the trigger when not firing the gun, he would as such never have his finger on the trigger while checking an ID.
When the Berlin SEK unit assaults the hotel Bourne just checked in to, some of the police officers carry Heckler & Koch G36A1 assault rifles (or, more accurately, civilian SL-8 versions of that weapon, mocked up to look like it). None of the German SEK units uses this type of weapon. It wouldn't make sense either, because it's too bulky for close quarters battle.
The banners carried by the protesters contain several spelling errors, including "Meer" (ocean) instead of "Mehr" (more). This is inspired from a real incident where the Germans protested against education budget cuts by putting spelling errors into their banner texts.
While Bourne was being detained in a Naples interrogation room, he ends up neutralizing both U.S. Consulate representative Nevins and the Italian police officer. After cloning the now-unconscious Nevins' SIM card, Bourne takes his keys. We know this because Bourne searches the parking lot for Nevins' car by repeatedly clicking the alarm remote, eventually finding the car in this manner. Why, then, does Bourne need a dent-puller to remove the car's ignition and start the car if he already has the keys?
During the car-chase through the Moscow tunnel, many cars are crashed and spun out. But there is a continuous stream of fresh traffic behind Bourne. After the first crash (or two), all traffic behind Bourne's car and the Mercedes would have stopped.
When the camera shows Alexanderplatz square in Berlin from a bird's perspective, a yellow tram enters from the left in the wrong direction with its back first and the electric pantograph on the rear end. Either they had a rehearsal with the tram going back and forth, or the cutter placed this shot running backward. Protesters are also digitally run over by the tram.
When Jason is grabbed behind the market by the police he spits vodka into the face of the first cop then the second cop swings his baton at Jason. When Jason blocks the swing you can see the baton "flex" revealing it's rubber.
When the 4WD crashes into the river Bourne is able to take one breath of air before it fills with water. He then struggles to escape from the vehicle, pulls Marie clear and attempt to give her mouth to mouth three times. He then sits underwater for a period of time. Whilst Bourne may be very fit and trained to work underwater it seems impossible that he would have been able to perform all this strenuous activity and provide Marie with three mouthfuls of air, all on the one breath. He should have drowned himself.
When Bourne is in the Hotel Brecker in Berlin, walking around the hallways and in some rooms, daylight is visible in some shots from the background windows behind the curtains. However, the scene was supposedly taking place at night.
During the chase scene near the start of the film, Marie gets shot in the back of the head, the bullet having entered through the back window of the 4x4. When we see the vehicle being pulled out of the water, the back window is intact.
When Bourne is burning Marie's photographs and the passports after her death, he is shown taking out what looks like 2 more passports and another photograph of him and her out of his back pocket. In the subsequent shots, he is shown only holding the photograph. This is evident when he folds it up.