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: When Jack The Ripper checks his watch before confronting H.G. Wells and demanding the key, the hands point to 8:50, the ensuing chase to the museum and demise of the Ripper may have used up a half hour or so, yet the time on the wall clock indicates that it is midnight.
Suggested correction: Movie time and real time don't match, so 3 hours has passed without all 3 hours being shown. The fact that the clock now shows midnight is meant to explain this fact without the need for subtitles to reveal the time.