Revealing mistake: When Hillard throws the basketball at Ripley, you can clearly see the white tape on Ripley's hand which was used to catch the ball. (00:23:10)
Continuity mistake: When Elgyn is going down the hallway picking up the guns, he finally comes upon a pistol. When he picks it up, there is alien slime all over it, but there is nothing else around him at all. Yet when the alien pulls him through the grating, there are gibs and assorted chunks of gore all over the place, which were not there only seconds before.
Continuity mistake: After Gen. Perez pushes the stacks of money towards Elgyn, they are right on the metallic edge of the table when the general offers a drink to Elgyn. In all of the following shots, the stacks have moved and are further in on the table, not on the metal anymore.
Answer: In Alien 3, Ripley discovers there was an Alien queen embryo growing inside her, so she chose to kill herself. By cloning her, scientist were hoping the Alien queen embryo she had in her at the time of her death would also become cloned, which finally happen after the 8th try. This is also why the Alien queen they extracted from Ripley has some human traits.
Bishop73