In the final fight, why did Michael tell the other passengers not to pick up the gun?
Since Michael doesn't have a specific tag, the other passengers could have been mistaken for Michael and shot as they pick up the gun. There's even a cut to the snipers outside readying themselves to fire.
Also in the final fight, why did Murphy prepare to shoot the other passengers down when he still thinks he's marked as a friendly? Wouldn't he be implicated in the shooting?
He could probably claim in hindsight that he was trying to get Michael and missed due to the stress of the situation; he'd be on leave for the shooting, but with the right backers he could get out of it with the equivalent of a slapped wrist.
And why did Murphy even bother finding Prynne among the passengers? Why not shoot everyone dead except for Michael?
He likely didn't have enough bullets to guarantee killing everyone, particularly when he was under observation from outside the train.