Character mistake: After Ryback was allegedly killed, Penn claims "we got him, but the SOB killed six men." Penn would not have known this, as he was with Dane the whole time preoccupied with Dane and his plans - he was nowhere near all the killings done by Ryback and never checked with his men at the time who was still accounted for. Also, it appears Ryback killed much more than just six by then anyway.
Visible crew/equipment: When the bad guys steal the helicopters and take off you can see the blades spinning at the top of the frame from the camera chopper during the wide shot of the other two choppers.
Other mistake: After Dane says to Penn "They'd shoot all the hostages", he says something additional but there is no sound - just his mouth moving from the side view as the camera pans to Penn's face.
Factual error: The terrorists supposedly stole the helicopters from a fictitious National Guard Base near Leadville Co. (No such base exists), but when they take off in the helicopters you can see the eastern slope of Pikes Peak in the background. Indicating that the helicopters are taking off from an airport just east of Colorado Springs.
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.