Bishop did it.
'I had to give him another shot for the pain' ...conveniently incapacitating the only witness.
Bishop is W-Y property, and will do as he's instructed by his superiors. He's also the only member of the landing team that is under no threat from an alien egg, because he is a synthetic and therefore 'unimpregnable'. I don't think a facehugger is going to be tricked and waste itself on a machine. Otherwise they'd be jumping out of their eggs at any sound or movement, so I think it's safe to say they can sense when something organic and compatible is near.
Coming back for Ripley and Newt makes perfect sense too...there's an extremely high probability that at least one of them may have been impregnated, meaning he could very likely return to W-Y with both the chicken AND the egg.
It's also very possible that Bishop is not conciously aware of his orders (or ensuing actions arising from them), thus giving him the perfect cover. In short, he may have had no idea what he has done.
I think this is the reason a synthetic was sent along...they are incapable of questioning orders.