[Spoiler] Plot hole?

It's an open question, and we can make educated guesses. Firstly, they may have only created life on Earth... if you assume that the first "engineer" we see is not part of the weapons program (his ship is discus shaped, not horse shoe shaped - I don't think that was trivial difference.) This script is not at ALL subtle about it's mythology, and its intend to ask the 'big question' of why we are here. If we look at the myth of the ancient Titan Prometheus, he stole a spark of fire from the Gods and gave fire to the mortals. This angered the gods, who punished him mercilessly. Our first engineer, may be interested in creating life, rather than making bio-weapons, and he sacrifices himself for this ideal, much like Socrates drinking the Hemlock, and losing his body, but gaining fame, and the spread of his ideas in western culture, including his oppostion to the 'might makes right ' attitude prevalent at the time. The Space Engineers seem to be well stocked in nasty weapons of mass detruction. They may have only visited other world to wipe them out, and only later found out, that someone had seeded Earth, without approval. It may be that other engineers from the discus checked in from time to time on us. And they left the directions to LV223. Perhaps at that time, it wasn't a military compound making bioweapons . When they do, somehow learn of the existence o the human racee, and a plan is made to wipe us out. It's not very clear of course. David didn't just see the map, there was audio on the hologram as well, so David listened to the replay of the briefing on the bridge. If the Engineers said the plan is to wipe out all life on Earth, he probably understood that.