The question of Whatney's survival was substitute narration, as already explained. As for freezing, his suit would have had to have not just an insulating effect but a heater just to be out during the -63C day.
Ruptured lungs is pretty much imploding. His capillaries would also rupture, starting with the ones in the skin and outer muscles and he would slowly bleed out internally, except for his lungs where he would bleed out in about a minute.
He was a botanist, so that he knew about hex without "knowing" hex is neither surprising nor egregious. The better question is why the hell didn't he have any music on his own laptop?
I really thought they explained he pointed the pathfinder antenna at one of the satellites, but I may have misheard/misunderstood that.
Simulating Mars gravity accurately would have meant putting not just Damon but all of the stuff he picked up, set down or dropped on a rig. That would have added considerably to the soundstage costs, which I'm sure were already considerable. Given that the movie was about Mars and not Gravity, I happily give them a pass on this one. They did well with the zero gee simulation on the Hermes, I think.
Sound is also a quibble. Almost everything was presented as being heard through the suit mics. The docking and EVA were bad, in that no one was tied down, and the guy crawling over the ship, while not unrealistically done, would have been better portrayed by using a SAFER pack.
I thought that the huge glass windows in the Hermes were the most unrealistic, unscientific aspect of the movie. Structurally not as sound, and a hazard for both radiation and micrometeoroids.
Regarding the punctured suit, during the incident in question on the shuttle EVA the astronaut was injured and his blood sealed the hole ( http://www.geoffreylandis.com/... ). The bigger question, I think, is how large a hole would be required to produce any usable thrust without being so large that there's no explosiveness to the decompression?
The slingshot and gravity assist were, clearly, not "genius" ideas, but more dramatic substitute narration. Unnecessary, but typical Hollywood, so shouldn't be a surprise. And they lifted a from a lot of other movies than Apollo 13 including 2001, various Star Treks, Aliens, and most directly, Lord of The Rings.