Other mistake: In the first Alien movie, a few drops of spilled Alien blood eats through two floors of the space freighter. Yet at the end of this movie when the Alien violently explodes and its entire blood supply is vaporized, the surrounding steel wall and floor are not affected. They do not melt, and Ripley is not affected by the blood spray even though she is only a few feet away.
Other mistake: I cannot remember the prisoner's name, but there's one guy who runs to throw the switch for the piston (he's wearing black I think) who Ripley has to chase down and stop from throwing the switch. He never dies. He is not escorted out with the others at the end. He simply vanishes after that scene and there is no suspected scene where he might have died because he is safely in the piston room. All other deaths (including screams) are accounted for by matching up who went where. Most were dead when he ran for the piston switch - only a handful remained and those are mostly caught on camera and are not him. As the company squad are escorting the other prisoner out he was not present at all.