Other mistake: At the end of the first movie Rybak is a Chief (E7), and he is a retired Lieutenant (O3) during this movie. Assuming he got commissioned to Ensign (O1) immediately after the events of Under Siege, it would take a minimum of 42 months to be promoted to Lieutenant. This movie takes place within 4 years of the first movie, because Admiral Bates is still the Chairman of the Joint Chiefs of Staff. The picture of Rybak in his Lieutenant uniform is at least 5 years old according to his niece. None of these timelines make sense for the rank he is in the movie.
Factual error: When the porter first gets ready to shoot at the terrorists (after Ryback falls off the train) he goes through a series of verbal instructions to remind himself what to do. The very first thing he says is "safety off". The problem is that the gun he is using is a Glock pistol. Glocks use a device called a "safe-action trigger" but they don't have a manual safety that you turn on and off.
Continuity mistake: After the train comes to a complete and lurching stop, the porter is shown being thrown forward into the bad guys as a lot of baggage falls all over the place. In the final fight scene as Ryback is entering the dining car, all the tables have all their place settings perfectly intact.
Plot hole: Now why the heck is one of the stealth fighters anywhere near the train? Stealth fighters use advanced targeting and do not need to be anywhere near their target, yet in the movie the one fighter is so close to the train when it gets blown up that it looks like it's on a collision course.
Factual error: The footage of the "Nevada Petrol Express" actually is of a similar operation that used to run over the Tecahapi Pass in Southern California. And "Espee" terminology never had "Petrol" in its language.
Factual error: The main premise of the film is ATAC's loss of control over their orbital weapon and their attempt to prevent it from doing damage. According to ATAC, they needed to know where the weaponized satellite is, so that they can lock onto it and send it a self-destruct order via radio waves. This isn't how the real world works: Radio waves emit in all directions from its transmitting source. The location of the satellite need not to be known; only it must be within the reach of the ATAC's signal.
Continuity mistake: When Ryback kills the guy coming out of the bathroom the lady who showed her broken bra to the bad guy stands in the corner with her hands covering her face, then her hands are on the side of her face, then her hands are back to covering her face.
Continuity mistake: When the train stops before the terrorists shoot the engineers the train stops on the switch track. But when we see the terrorists with the red flags the switch track is behind them. (00:18:45)
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.
Deliberate mistake: During the scene where Ryback is fighting Penn (the grey-haired mercenary) in the kitchen, watch for the shot where Ryback flips Penn. The film has been sped up and the result looks disjointed and out of place. The characters are moving FAR too fast for it to look natural.
Continuity mistake: When Bobby Zachs steals the CD, Ryback is seen with him outside the train car making their way to the next car and the train is still going about 40 miles per hour. The scene changes to back inside the train with the bad guys and the window in the background shows the train traveling about 5 miles per hour.
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.
Visible crew/equipment: When Ryback throws the exploding bomb into the car that the bad guys are in, one of the guys bursts into flames and you can see the white fire safety mask that he is wearing.
Continuity mistake: As Ryback approaches his fight with Penn he unloads his gun and puts the empty gun on the table (separate from the cartridge). But then as he runs through to free his niece he picks up the unloaded gun and then uses it shortly afterwards without ever reloading to shoot Dane.
Other mistake: In the scenes that show the satellite in space, there are collision lights visible. It's not like there is anyone up there that is going to fly into the satellite if they didn't see the collision lights.
Other mistake: Captain Garza is listed as Colonel Darza in the credits.
Visible crew/equipment: At the beginning of the film when all the personnel leave the control room, you can see the boom mike visible in the reflection at the top of the glass.
Continuity mistake: When the kitchen is shot at by the bad guys, the chefs inside do not get hit as you can not see any blood, but when it goes to close up, they are ridden with bullets and blood is everywhere.
Plot hole: When Casey determines to hot-wire the Chevy truck, he raises the hood, grabs two bare wires on the passenger side of the engine, rubs them together, and the truck starts. However, this is patently impossible since the ignition is in the off position. The engine might crank, assuming he magically found the hot lead to the starter solenoid, but it would not start.
Revealing mistake: Look for the blatantly awful special effects when the main bad guy is falling into the flames.
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.