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: During the thunderstorm at the end, the thunder comes every couple of seconds, it doesn't correspond to the lightning at all, and it sounds exactly the same every time.
Audio problem: When Holmes and Watson are about to go out to the Blackhorse Tavern the second time, Holmes answers Watson's question as to where they're going by saying "the Blackhorse Tavern." However, his lips do not move.