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: According to the commentary on the DVD, Ridley didn't add this scene to the original cinematic release because he thought it revealed the true horror of the Alien too soon in the film. The scene is quite early in the film and he thought revealing the fully matured Alien at that time would reduce the viewer's fear.
I had watched Alien several times before I noticed the Alien hanging there.At this point the Audience have no idea what the Alien looks like, they're looking at pieces of science fiction equipment put in by the production crew that they can't relate to, so for all they know the Alien could just be a piece of kit hanging there.