Revealing mistake: Whilst Bourne is following the assassin and drinking his water, he passes some toy windmills. Just before passing them there is a group of people behind Bourne and you can see many are staring towards the camera. (00:11:25)
Revealing mistake: When the demonstration crowd is assembling in the plaza, there's a yellow tram entering on the left hand side. Watch as someone walks across the tracks in front of it and disappears through the corner of the cab. The shot must be a composite of the crowd amassing and the tram shot separately and then overlayed.
Revealing mistake: Early in the movie during the scene which Jason Bourne is being detained, the person from the Consulate while questioning Jason Bourne gets interrupted by a cell phone call. He has a Hand Spring PDA/phone and during the phone conversation you can see a red light flash on top of the phone. If you own one of these phones you know that means you have no cellular signal. How could he be having a phone conversation if he has no signal?
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.