Question: At the end we are left with the question of the pilot's intentions, and what happened. Is he going to help them, or pull an about-face and machine-gun them down thinking they're infected?
Question: Do you know what the pilots say (and what language) at the end?
Answer: It's Finnish. They say "Lähetätkö helikopterin?" which means "Will you send a helicopter?"
Question: In the beginning, there are several shots of riots, seemingly stock footage. One shows a man hanging and people beat him really hard to death. It was short, but quite disturbing. Was this real footage? If so, what was the real incident?
Answer: None of these shots are real footage; it was scripted and shot for the movie, made to look like newsreel/raw footage.
Question: Why did Jones fire at the ceiling when Clifton is attacked by the infected Mailer?
Answer: Because he is incompetent and doesn't know how to fire the gun properly. When he tries to shoot Mailer, the recoil takes him by surprise and he stumbles backwards, still squeezing the trigger, spraying wildly upwards.
Answer: That question is actually answered. The pilot is speaking Finnish, and he says into the radio "lähetätkö helikopterin" which translates as "Can you please send a helicopter?" Looks like he was actually helping them after all, and there is still some civilization (or at least people with radios and helicopters).