alien distress call.

SNARK I think Ridley for the director's cut did not wanted to point out too much at Ash, because now any kid watching the movie for the first time may guess that he is not trustworthy and has a secret agenda for the company. Actually he also omitted the scene where Dallas asks mother how to terminate the alien and she only answers " unable to compute " For the Weyland Yutani theory, is way too complicated already because everyone is trying to tie in with aliens and alien at the same time, even if they hate aliens

in fact, according to commentary by Ridley Scott as well as Dan O'Bannon, Ash being an andriod and the whole "company knows" was added to the script by the producers. originally i believe the crew was just woke up because they picked up a distress signal. the idea of the company knowing about it and sending them there to bring back lifeform was kind of dropped into the script at a later stage. im not sure if that also include the signal being deciphered as a possible warning or not though... but it may explain the loopholes a bit

oops, somehow i missed the fact that his was already mentioned above