Plot hole: When Daniel is in the air with the stolen plane from the Los Alamos air base Nat suddenly appears from behind. However, Nat had no chance to slip into the plane secretely as there was only one stepladder that had been in his mom's full view while she hugged Daniel good-bye. (01:25:30)
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.
