Looks to me like David (who is reported to be really intrigued with this "life-making" technology of the Jockey) might actually become the aforementioned "Maker of the Xenomorphs"/Prometheus.
Whose not to say that in his quest to become a real human he starts tampering with all the Jockey-tech? And accidentally "creates" the Xenomorphs and plants them back on the Jockey ship or infects the little egg-like devices we see all over the Jockey ship which then turn into the eggs?
From there, that can explain why the Jockey got face-hugged, the crashing ship, etc. and perhaps the "infected humans" we see earlier are David's failed experiments?
It also can explain why Weyland Corp. has knowledge on what transpired, both through David and what other flight records...setting up for the casual "fly-by" of the Nostromo.