Plot hole: When Ripley goes to access the computer Mother, the entry door opens and closes with a hissing noise, a couple of minutes later you see Ash next to Ripley with a smile on his face. How did Ash manage to open the same door without it making the hissing sound? Ash could not have been in the room before Ripley came in - once Ripley has sat down at the console, it rotates on a 90 degree angle, this would have made it impossible for Ash to be hiding behind a desk or a computer console without being seen by Ripley. There are many doors on the ship that make the same hissing sound when the doors open, an obvious example is the infirmary door. And Ash couldn't have disabled the pneumatics of the door, because when Ripley exits the room, the hissing noise is heard again. (01:18:40 - 01:20:00)
Plot hole: The shuttle "won't take four" crew members. Considering it only has two cryotubes (and hypersleep appears to be necessary for any hope of survival), it doesn't seem to accommodate three people, either. (Admittedly I would still go for it, too, if I were up against a 7-foot-tall acid-blooded alien monster with two sets of jaws, but there doesn't seem to be much difference whether there's three or four people onboard).
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