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 the crew are dining together just before Kane meets his grisly end, the scene cuts from a long shot, where Parker is saying something, to a closer shot, with the conversation continuing as before. The problem is that Parker's voice can still be heard, but his lips aren't moving.
Audio problem: When they are looking at the molecular acid eating through the decks of the ship from the facehugger, Parker says the words "Take a look at this man!", but his mouth is saying something completely different and much shorter.
Answer: It's another race of space alien that is also subject to infection by the Aliens. This particular one was infected and moved as far as it could from its race's known space and broadcast a warning before it died. The presence of eggs in the hold may indicate that it was a research ship. The race was never used in other Alien movies because it adds a new dynamic to the plotlines: two alien species, locked in mortal combat and neither particularly friendly with humans. In the Alien pseudo-prequel Prometheus we learn these beings are known as the Engineers and have interesting ties with both the aliens and humans as well.
Phoenix