Continuity mistake: Just after the doctor started the post mortem on that little girl, the front of his gown is covered with blood. Yet, a few seconds later, after the two other guys appear, his gown looks better, with less blood. And during the whole post mortem scene, the blood spot actually changes its size a few times. (00:17:55 - 00:19:55)
Continuity mistake: In the cafeteria scene, Ripley gets a square of what looks like cake and pours half a glass of orange juice. When she sits down her glass is full. (00:27:00 - 00:27:50)
Revealing mistake: In one scene, two of three prisoners get killed by the alien. The last one is sprayed with blood and tries to escape in panic. With his left arm, he leans upon a half-open, hydraulic-powered metal door. However, it moves a little to the left, and as the prisoner takes his hands off, it immediately snaps back to the right. Now even if you suppose that there was no hydraulic pressure behind it, it should not have moved to the right again. It is very obvious that this door is just a light-weighted part of the scenery. (00:43:17)
Audio problem: Right before the people from the company enter the prison, Jude is being chased by the alien. He yells, "Help me.", but his mouth is wide open and the words don't match the movement of his lips. The same thing happens when he yells, "Please" shortly afterward. (01:31:10)
Revealing mistake: As Ripley and Dillon lure the Alien into the piston chamber, Morse closes them just in time. Watch closely - he misses the switch. (01:38:15)
Audio problem: When Aaron attacks "Bishop II", he yells, "F***in' android.", but the words don't match the movement of his lips. (01:41:45)
Continuity mistake: Any shot of the alien which isn't made using a guy in a suit has a green glow around the alien's body but any guy-in-a-suit shots do NOT have a green glow.
Other mistake: The alien that comes out of the dog is a lot bigger than the actual dog just seconds after it appears. This only applies to the theatrical version, as in the extended version the alien comes out of an ox.
Continuity mistake: When Ripley gets out of the sprinkler water at the end of the movie, her clothes are soaking wet. Immediately afterwords, when she's talking to the man from the Company , her clothes are much drier.
Plot hole: One alien egg is shown hanging from the wall at the start of this film, yet there's no way it can be there. The queen didn't take any with her from LV426 in 'Aliens', and if she did, she had no opportunity to place them on the Sulaco between exiting the dropship's landing gear, engaging Ripley and being killed.
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.
Continuity mistake: When Ripley is looking for the Alien in a room full of pipes and chains, she spots what looks like the head of the Alien and slowly walks towards it, talking to it as she goes. When she smashes it with a metal pipe, loads of bugs fall out and it's a completely different pipe we are looking at, it's not smooth and long but a corner piece.
Continuity mistake: Right at the beginning, Ripley has a bloodshot eye and a blown pupil, but they both vanish far too quickly; it takes lots of days, certainly not hours or one day.
Answer: Agreed the Queen could have stowed the eggs away on her body as Alien bodies, especially one her size, could easily have a couple of eggs hidden upon her, and we would not know. They are masters of disguise these creatures and can merge in with their own environments or others...what's to say an egg can't look like part of the Queen's body? In addition, could Facehuggers not attach themselves to the Queen's body and merge with it somehow? Flatten themselves against her skin maybe?