Dr. Shaw (and her boy friend) told the crew of Prometheus in their presentation that Engineers left - as far back as 35,000 years - clues as to the location of their planet in the form of a star pattern in images found all over the globe.
"They want us to find them" - Dr. Elizabeth Shaw
When they researched the pattern, they found LV-223.
LV-223 was NOT their home planet, it was their secret military base dedicated to project "Kill 'em all!"
The base on LV-223 looked to be a temporary installation from 2000 years ago, NOT a permanent colony from 35,000+ years ago (I don't have canon proof, just the impression I got from the movie).
It seems like the wrong place to leave directions to on both accounts.
Is there some canon explanation (movie detail I missed, interviews/deleted scenes) that explain this seeming contradiction?