With thanks to an unnamed source who drew this article to my attention, here's a link to a piece in The Guardian that attempts to explain some of those plot holes in Ridley Scott's Prometheus. I was relieved to see I wasn't the only person stumped by the meaning of that first scene.
Puzzled by Prometheus
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I thought that this was a pretty funny take on the plot holes:
http://boingboing.net/2012/06/16/plot-holes-in-prometheus-deli.html
Haven't seen the film yet, but this post sounds familiar, given that one of the screenwriters is Damon Lindelof, one of the two main writers behind "Lost."
If it was only the first scene you had trouble following, my hat is off to you.