It was done to give credence to a third movie. The Aliens are just capable, nuff said. That's what we are expected to take on faith.
If it has to be explained any other way, it's better to say Bishop had a hand in it. It wasn't malice on his part, he was just doing what he was told to do. He had the time, the ability, and had already been told once to take care of the specimens for return.
How the egg got upside down? That's an alien 3 script issue. How they got on board? Bishop, all the way. Why even bother including footage of him being gone otherwise? Why make it a thing? He could've been waiting right there the whole time and the movie wouldn't have made less sense or anything.