This question is a little complicated but I will try to outline problem as neatly as possible.
In Alien, the crew of the Nostromo land on a planet, find what we would now know to be an Engineer ship, and inside that Engineer ship there are face-hugger eggs.
In Covenant, we see that the Engineers were wiped out by David when he arrived on the Engineers' home world, and he then set about developing the xenomorph life form.
Here's the problem though. The face-hugger eggs did not exist before the Engineers were wiped out. David worked for a long time after the extermination of the Engineers to create the face-hugger eggs. So how did a bunch of face-hugger eggs end up on an Engineer ship, wrecked on another planet?