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 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: 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)
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.