No it does not. The opening sequence of the movie indicates the Engineers have existed for quite some time. it is implied they gave the genetic material which became all life on Earth. This fact alone makes their species very old indeed. Even if the Predators had been using the Xenomorphs for a long time as AVP suggests (20,000 years at least) the Engineers have been around for at least 1000 times that long.
When we meet the Engineers and their technology in Prometheus, it is clear the creature or some variant of the xenomorph is already known to the Engineers. It is part of the bas relief on the wall of the giant head room (see below). If we are to assume the Engineers are the artists (which there is neither confirmation or denial of) for that art to exist, someone had to know something about the creature and presumably its lifecycle.
Xenomorph Bas Relief in Giant Head Chamber
If the Engineers did not create the art, then perhaps they did NOT know about the xenomorphs but seeing how the creatures came from the development of the Black Ooze in a human host, which then is transferred to another human, gestates in the body of the second human, is extracted and eventually uses a third alien to come into existence, AND the Engineer's ship is filled to the brim with canisters of the Black Ooze, it is safe to assume even if the aliens did NOT create the bas reliefs, they knew the potential of the Black Ooze and its inevitable results.
It is safe to assume the Engineers know the origin of the Xenomorphs even if they did not specifically create them.