Minor Plot hole: A court of inquiry does not find Ripley’s account regarding why she destroyed the Nostromo credible. The aliens are believed to be from her own imagination to cover-up from the fact that she destroyed the spaceship herself. But somehow, the death of the other six Nostromo crew members is not brought up. If she was in fact responsible for the destruction of the spaceship, she would also be responsible for the death of the whole crew and tried as a murderer. Hollywood legal court magic? Yes.
Minor Plot Hole: Apparently Ripley can hang on to a ladder while a power loader mechanical-suit, an alien queen and the vacuum of space itself are pulling against her. It would be an accomplishment to last a second with any of those 3. When did Ripley get this super strength ? It’s not the fourth movie yet.
Major Plot Hole: Hicks knows the aliens will breach their perimeter sooner or later, yet no one suggests getting to the other dropship until they learn of the imminent nuclear disaster. So they were just going to sit there for 17 days with next to no ammo and 150 pissed aliens trying to get in if the reactor didn’t go critical ?
Major Plot hole: Burke’s plan was to impregnate Newt and Ripley while they slept, then sneak the creatures through quarantine in their stomach and jettison the marines in space. But Ripley and Newt would realize they were impregnated when they would have awaken with facehuggers attached to them. How would he hide that? Everyone would know it was him since he moved Ripley’s pulse rifle out of the room, something facehuggers aren’t prone to do.
Plot contrivance: In the future there is no nuclear safety and no fail-safe procedures. Just a few bursts from a Smart-gun can cause a nuclear power-plant to explode in a way the nuclear material used in those plants is not capable of doing.
Retroactive continuity: In the first film, a few drops of alien blood melt through several floors of the Nostromo. In this movie, when the sentry guns mow down several aliens, there is no structural damage/melting on any of them.
Unnadressed Issue: Just how did little Newt survive for so long alone and surrounded by deadly aliens? Most soldiers can’t last more than a few seconds. I know we all want that cute little girl to survive, but not showing how she managed to live for days in the most hostile environment of the sci-fi future is a sign in itself that the screenwriter had no clue himself.
Unnadressed Issue: The military technology at the disposition of all space marines is lacking even in our modern standards. They have no night visions, no armor and simply no technological advancement that would differentiate them from current American soldiers. In fact, Hicks uses a shotgun that is 200 years old, akin to soldiers in Afghanistan today using muskets. Was the defense budget of the past two centuries blown on spaceships and nothing else?