Revealing mistake: When the villain finishes his 1st appearance in the Pentagon's videowall (with the fake Eiffel Tower on the back), the screen turns black when he finishes his statement. However, when the camera turns to the Army men present, you can see the reflection of the villain's face on the glass.
Revealing mistake: The actor who plays Tom Breaker is quite easily the worst impersonator of a smoker. Clearly not at ease with holding a cigarette, he also doesn't ever appear to inhale the cigarette smoke either.
Revealing mistake: Look for the blatantly awful special effects when the main bad guy is falling into the flames.
Revealing mistake: When Bobby opens the door to grab the CD from the computer look at his right hand, he already has the CD before he's taken it out of the computer.
Revealing mistake: When Ryback is fighting the grey-haired bad guy in the kitchen, the bad guy is losing and spots a meat cleaver on the counter. When he quickly picks it up, holding it at head level, you can see the cleaver blade wobbling from side to side. An obvious rubber prop.
Revealing mistake: Before Trillings and Gilder enter their passcode for the first time at ATAC there's a screen showing the codes already entered and the transfer completed before they've typed anything.
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.