A few things I noticed watching the film the second time around:
Did anyone else notice that when the crew returned to the dome for the second visit, David was following behind in one of the smaller dune buggy vehicles as he was going off on his own to check out the possibly malfunctioning probe. As the larger transport passed inside the dome walls ahead of him...way ahead of him, David slowed to a complete stop, roughly over the hangar bay doors of the Engineer ship. The camera stayed on him for a few seconds as he was stopped, then cuts to another scene. At first I thought this was just a David "moment" as he looked at the view, but I think there is more to it than that.
When the Prometheus goes into orbit, after Shaw and Holloway's meeting with Vickers, we see a scene of the crew doing scans and such on the planet, including David sending transmissions trying to get a response from the Engineers (the "provided your thesis is correct" scene). I got a good look at the holographics of what he was sending. Looked like something from the Voyager space craft messages. Lots of different things from different cultures, music, art, DaVinci, et cetera. Seems he was trying all the languages the Engineers may have possibly learned on Earth. I think I spotted an image of Linda Blair in her exorcist makeup in there too
This one was easy to spot the first time, but paid extra attention the second time as people were complaining about it. As they are entering the atmosphere and the female scientist is telling the captain about the atmosphere and surface content, one of the two other guys in the bridge crew says -
"Bringing data up. We've got a couple of hard spots. Could be metal"
Then we get a minute of various scenes showing the ship passing over lots of different terrain just above the planets surface. Read as = many hours of elapsed time as they search for the "metal".
"No radio and no heat source."
Then the captain tells them to go through the gateway between the rocks, just prior to visually confirmation of the domes. They had been searching for those "hard spots of metal" since entering the atmosphere. They appeared to be in the graphics of several of the monitors in these scenes as well.
How many times have you seen it stated how ridiculous it was that they just
"happened upon" the Engineers domes without having to look for them?
When Shaw tells the captain "we're going in" as they enter the dome, he says "copy that". His lips don't move Got to have on of those in every Ridley Scott movie.
When Shaw tells Holloway "Don't be an idiot" as he is unfastening his helmet in the waterfall room, he replies "Don't be a skeptic". As others have noted, he believed he was about to meet his maker, and did not think for a second anything would harm him in this place.
Now as to why the rest of them then proceeded to take their helmets off...That should have been handled better in the film.
In the cave after the waterfall scene we get this dialogue:
"It's minus 12 in here."
"So why is this water not frozen?"