1) Given the fact you clearly see troodon as you enter the visitor centre it's safe to assume thats what got them; though I'd wager it may of been the ptreadons or rex that took the chopper down since it seemed more mauled than simply crashed from a hallucinating pilot.
2) It's never said it was shot down, just it went down and there was shooting. See above answer for 3 possible answers.
3) It was an incendiary grenade, the one he uses in episode 4 to try and kill Nima, Jess and Gerry
4) Trophies/Achievements is referring to the PS3 and xbox versions; where all games have trophies/achievements to complete.