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)
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.
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.
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?