Corrected entry: In the scene where Ripley and the doctor perform a post mortem on Newt, they cut her open and blood flows down the drain. If it comes into prolonged contact with air, or the "user" dies, the blood should clot, and not flow like this. Even if this is wrong, they just took her out of the freezer, so she should be at least partially frozen.
Corrected entry: At the beginning of the film, the camera shows one egg, but then the movie shows two facehuggers.
Corrected entry: Just after the post mortem, or autopsy, Superintendent Andrews enter. Ripley wants the bodies to be cremated but Andrews says that they'll be put on ice. Later when they discuss, who should be leader (chapter 16 on the DVD), Morse tells Ripley about things that don't work. He also mentions the freezers, so how is the Superintendent going to put the bodies on ice, if the freezers don't work? And if the freezers don't work, how come the morgue's freezers work?
Corrected entry: In the credits - and the warden says it - they mention chromosome YY, or double YY. But that is impossible; women are XX and men are XY; you have to have an X chromosome, sometimes you can have XXY, and maybe there are other variations, but there must be an X, no matter what.
Corrected entry: How did the stowaway facehugger impregnate the dog (or ox, depending on which version of the movie) after it had already impregnated Ripley with the Alien Queen? Alien 1 & 2 had already established that facehuggers die shortly after impregnating a host. Not only would it be impossible for the same facehugger to impregnate 2 hosts, but it should have died after impregnating Ripley.
Corrected entry: When the prisoners are being chased by the alien in the corridors, it is seen that it runs much faster than the prisoners, yet can't catch them. Sometimes the alien is shown right behind them but when it switches to the alien's sight, you can see it is further away.
Corrected entry: How come the alien eggs in all the films look different? At least the ones in the first three films should be looking the same since they came from the same queen.