Audio problem: In the scene where Kalgan confronts third engineer Steve Godell on the catwalk, he laughs before saying the line: "third engineer Steve Godell?" The laugh begins while Kalgan is obscured by the set, and continues as he moves into the scene. As he steps from around the corner, you can see his mouth is closed and not moving at all, despite the fact that his laugh can still be heard for 3-4 seconds.
Audio problem: When Bourne rescues Marie, he fires a silenced pistol at the man who was trying to rape her, but the sound is of an unsilenced gun. (01:01:10)