The sound heard from the helicopter is that of one with a 2-bladed main rotor (Bell 206 JetRanger or UH1 Huey). But the helicopter depicted (N35961) is an Airbus/Eurocopter AS350 (H125) and has a 3 bladed main rotor which makes a much different (smoother) sound.
When Mulder is shouting Scully's name after she leaves with Doggett in the helicopter, the second time he shouts it his mouth isn't moving except to swallow.
When Scully shoots the Alien Bounty Hunter neither her, Doggett or the other agents are affected by the alien's blood which has been shown to burn nearby humans. This is however seen having happened to Skinner in the preceding scene when Doggett finds him in the ceiling space.