My problems with Prometheus are not generally of the 'mystery' variety. I am not super hung up on the loose ends left by the story, the unanswered questions. Mostly I'm annoyed at the excruciatingly stupid character actions and the general lack of motivation - which many have read as 'mysteries' but which I read simply as bad writing.
One 'mystery' that did bug me was the question of what David said to the Engineer at the end of the movie. Whatever it was, it sent the Engineer into such a rage that he tore the robot's head off and beat Weyland to death with it, so it must have been a helluva statement, right?
Not so much. Here's the translation:
"This man is here because he does not want to die. He believes you can give him more life."
That comes right from Dr. Anil Biltoo of the SOAS Language Centre in London who served as the Linguist Teacher on the film, so this guy knows what he's talking about. According to Dr. Biltoo, who was interviewed by The Bioscopist, there was a larger conversation - yes, a back and forth - between the two edited out of the movie. Perhaps that longer sequence holds the keys that explain why The Engineer was such a roided out dickhead. Hopefully it turns up on the Blu... with subtitles.