Audio problem: When Mike is outside, in the strong winds, yelling "Jody," his mouth doesn't match up with the audio, and sometimes his mouth doesn't move at all. (01:12:00)
Audio problem: When Tom Skerritt first "interfaces" with Mother after being awoken, he says, "Good morning, Mother" - it is not even close to being Tom Skerritt's voice. According to the book 'The Making of Alien' this line was dubbed in by Ridley Scott as Tom Skerritt wasn't available at the time.
Audio problem: When Wells is en route to the Hyatt, exhaust sound from the taxi as it descends the hills of San Francisco seems to have been stolen from the Mustang in "Bullet." When the taxi pulls up in front of the hotel, it sounds again like the ordinary taxi that pulled away with Wells earlier.
Audio problem: When Bond is being shot at while motor-boating away from his pursuers in Venice, at one point during the chase, they shoot right next to a rope on his boat and a sound from a silenced handgun is heard when the bullet hits the wood. No one is using a silenced handgun.