The amount of Radiation was too much. Plus maby they thought because of the blast, the ship would no longer be there.
But even better maby you just didnt read what i sied? The Company have Gone back to the Crash site because it suvived the blast because of the reasons i sied above in my other post. And have built a Complex around it. So the company can study the Eggs and do whatever they want. But as the Ship who was going to collect the aliens from the base and return it to earth gets blasted by a predator ship, Crashes near the base which forces or allows for the aliens to get loose.
Alien 3 takes how long after Aliens? a week yeah? so while the company is building a new Complex around the ship ready to study and bring back the eggs on site. And because hugh ass buildings like that take a good few years to make. The company knowing of Ripley thought it could get the alien faster by going to her.
And OFC when has the AVP Movies ever tied itself to the movies perfectly? It's a Seperate universe which hardy classes as Canon. Even the games are not cannon if you follow the movies plot. Apart from a few details at times the movies hint at. Look how awesome the games are. If AVP3(The movie) follows its own plot with Spaces Marines, Aliens, Predators within the universe but stays true to the franchise like both games have done. Then it would be a good movie.
Anyway if what you say is true then by theory they shouldnt be any AVP Games or comic books, since the crash site was destroyed if they followed the movies plot as cannon. Which the games doesnt
Your're gonna have to cut corners if you want a Movie about Space marines, predators and Aliens like we all do. Or do you want another AVP Movie set on earth with a bunch of townsfolk getting killed? And a setting no one cares about or wants?