Who's to say?

Something I just thought of- In Alien there is a hole in the flight chamber that gives way to the hull of the ship where we discover the eggs. Yet in Prometheus the way they enter the ship is directly through the facility that sits on top of it- so logically they do explore far more of the ship than what was explored in Alien. So it stands to reason that the canisters of black goo were on LV-426 in a separate hull, and vice versa for Prometheus. We see that the engineers obviously know about the xenomorph (or the Decon at the very least)- and maybe that is what they were out to create overall. David's line "sometimes to create you first have to destroy" supports this a bit. I'm happy with the movie- even without this explanation- just waiting for the sequel.