Audio problem: At the beginning of the movie, the terrorists start take over the train, Ryback beats up a terrorist and throws him out of the train then some guy says something into the radio like, "we got one casualty", his mouth doesn't match what he's saying.
Audio problem: When the mercenaries begin to take over the train one of them grabs an older woman and the small child with her. The bad guy threatens to "shut that bitch up or I will", but what he says doesn't match his mouth.
Audio problem: When Ryback is making his bomb, he puts a glass inside a sweater and wraps it up and then smashes it. The sound of the breaking glass isn't muffled as you would expect, it sounds like glass breaking and spreading out over a surface.
Answer: I would say yes they where planning on killing some of the mercs. There is one fact that shows that. if they had plan on putting all the mercs into the copter, then the guys in the engine car should have know at x time get out and move back to get into the copter, giving the fact that they are still in the engine car when it hits the other train tells me they didn't know.