C.) Captain Janek (Idris Elba) must not care about his stranded crew because he goes off to have sex with Vickers (Charlize Theron) while the marooned men are in danger. If we gaze at Janek, his character arc is essentially one in which he goes from being "just the captain" (and indeed, not caring), to laying down his life to save the entire human race. He comes to understand, because of the events on LV-223 that he can no longer remain uninvolved, or on the side-lines. All that century-old music he appreciates from Earth's past (his parental figure or most important influence, it seems...) will be lost to the ages if the Engineers have their way. If Janek had remained at his post all through the night, this character arc would be sacrificed. And thus his final act would be less meaningful, and less surprising. And besides, Janek doesn't see the team, necessarily as "his" crew. He's just along for the ride...until something he cares about is threatened. Again, this isn't Captain Kirk-styled heroics; this is a very real, unromantic human portrayal.
D.) Shaw blows up an Engineer head, willy-nilly! Early in the film, Shaw recovers an engineer head, sticks some electricity in the thing, and blows it up. I've seen a lot of folks complain about her behavior in this scene. But if you look more deeply at the symbolism of this sequence, it doesn't seem so baffling. The Engineers are clearly afraid of their creation, the humans, and exhibit A might be this very moment. A human shows up and in a fever to gain "the ultimate knowledge" she destroys that which she seeks to understand. Could be a metaphor for the whole movie, no? In trying to comprehend God, do we destroy God? In finding God, do we destroy faith? Similarly, look at the decapitation symbolism, specifically. A decapitation can mean a number of things, like for instance that your head and heart are not connected. Some scholars also interpret decapitation imagery in dreams to mean that the dreamer's beliefs are under attack. In a very real way, this reflects Shaw's situation (and her character is already connected explicitly to dream imagery in the text of the film...) Her chosen belief is that the Engineers are God. She finds out that they are not. The severed head is both a literal and metaphorical reminder that her beliefs are wrong. The Engineers are clearly as mortal and vulnerable as humans. Finally, this scene functions as an eerie mirror of a similar scene in Alien involving a decapitated Ash, and attempts to communicate with the damaged android. In any case, engaging with the film's mode of communication makes this scene less irritating, and more provocative.