Continuity mistake: In the Moscow car chase, Bourne's car is hit from the driver's side by a patrol 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. (01:25:25)
Continuity mistake: In the Moscow car chase, when Bourne's car is hit by a FSB Mercedes which had been hit by a truck, the whole exhaust section of his vehicle is seen collapsing to the ground. In the next shot, the exhaust section is perfect. (01:27:50)
Continuity mistake: After escaping interrogation Bourne switches SIM cards and throws the phone back down with it facing down. When we see the American awake the phone is now facing upwards. (00:30:10)
Continuity mistake: When the assassin is following Bourne in Moscow, he stops on a bridge and shoots at Bourne, a second later, when the Moscow police arrive to detain him, his car is not on the bridge anymore. (01:25:50)
Continuity mistake: In India when Bourne is running away from the assassin, every time the camera cuts to him we see him run past the same toy windmill stand. This happens three times. (00:11:10)
Continuity mistake: When Bourne is being chased by the assassin, he leans his seat back all the way in order to switch seats with Marie. After they switch, in the next shot of Marie the seat is back up and she has a seatbelt on. There was no time to do either of those, much less both. (00:15:00)
Continuity mistake: During the scene where Jason Bourne interrogates the girl from Paris in a tram tunnel, her hair keeps changing from camera angle to camera angle. In one angle, it's off her face; in another angle, it's disheveled and covers the right side of her face.
Continuity mistake: When Bourne pushes Ward's head to the table and says, "I told you people to leave us alone.", you can see Ward's glasses. Two shots later his glasses suddenly disappear. (01:12:45)
Continuity mistake: In the chase scene toward the end, both Bourne's and the assassin's vehicles are racing down a tunnel. Both of them run several cars off the road while passing them, which should block traffic behind them. Instead, in one long shot of the tunnel, a ton of moving cars can still be seen directly behind them in the tunnel as if traffic was completely normal. Furthermore, even if there was room to drive around the obstructions, nobody thinks it's a good idea to back off from two cars smashing into things?
Continuity mistake: When Bourne does in Berlin the online research in the newspapers about the two murders he is accused of, in the first shot (over Bourne's shoulder) the first word in the entry mask of the search engine is "Medienprodukt" (which, by the way, is a verbatim but bad translation of "media product" and no German would say that). Also in the field "Jahr" (= "year"), we can see that the numbers "198" (instead of 199) have been entered. In the next shot, the close-up of the entry mask, "Medienprodukt" has switched to the better translation, "Medium". The entry in the year field has switched to "1997 - 1999". (00:57:35)
Continuity mistake: When Bourne makes the call to Pamela Landy from the rooftop, we hear him talking about Nicky. When the camera switches to her, we see she is across the room, away from Pamela. In the next shot, with the view from outside the window, she is standing right next to Pamela, and then moves back again in the next shot.
Continuity mistake: The damage to the taxi in Moscow is constantly changing. Noticeably a massive spider crack in the windshield that disappears in the wide angles.
Continuity mistake: In "Identity", Marie has a tattoo on the upper right shoulder portion of her back. In the beginning of "Supremacy", she is walking in a bikini top. We see her back for a few seconds and there is no back tattoo, only the one on her right arm.
Continuity mistake: The blue Saab convertible belonging to the Berlin-based assassin is parked with all wheels on the road when the call-in team arrives in a silver 4x4. Shortly afterwards, the same car parked almost completely on the sidewalk when the assassin's house explodes. (00:41:50)
Continuity mistake: During the Moscow car chase, Bourne hits two barriers that slide through the intersection, one being on its side. In the next shot, the two barriers are gone and the cars at the light change as well.
Continuity mistake: During the car chase in which Bourne gets shot in the shoulder, his hands get covered with blood, but in several shots his hands are perfectly clean.
Continuity mistake: When being pursued by the Russian agent in India, the girl is shot through the rear window of the vehicle. Yet when the vehicle is pulled out of the river, the rear glass is intact.
Continuity mistake: In the main car chase through Berlin, Jason's car is T-boned by the Russian assassin's black Mercedes 4x4. We see a shot of the car spinning and the back bumper/fender is hanging off, held on only by it's very tip on the left hand end and dragging behind. However, in all subsequent shots it's still attached.
Continuity mistake: At the start, the first wire put into the right most portion of explosives changes position between shots.
Chosen answer: They frame Bourne because Borne was actually the one who killed Neski and his wife (he was doing it on Conklin's orders). Once Pam Landy does some digging, she will realize this; then it's a simple matter of putting two and two together - the man who killed Neski would obviously have a huge motive for covering up his crime. This is why Abbot and Gretski frame Bourne: he's the perfect fall guy.