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.
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)
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.
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.
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.
Continuity mistake: Admiral Bates has different ribbons from the first movie to this one. Not only does he have at least five additional ribbons (which is possible), but certain awards have disappeared altogether.
Continuity mistake: When Travis Dane went on the computer to switch tracks to begin the course for the head-on collision, the monitor displays the green trail swapping from the upper track to the lower track. In the next scene where you see the train passing over the switch track, it went on the upper track.
Continuity mistake: When Casey Ryback is heading towards the start of the train, Penn asks his henchman to check the roof of the carriage. In the first shot a man gets up off his seat and another one takes his place. In the second shot when the man is outside making his way onto the roof, you can clearly see that the other man has not moved from his position, let alone taken his place.
Continuity mistake: This happens when they stop the train in order to get the CD that was confiscated by Steven Seagal. A moment or two after the train comes to a complete stop, Travis Dane explains how important the disc is - if you look behind him you can see the scenery outside the window still moving very quickly.
Continuity mistake: When Captain Trilling enters the room where Captain Gilder is waiting for him, she says "Have some champagne, Captain Trilling." When she says this, she has the wine glass in her right hand. A split second later, as Captain Trilling gets close to her, she has changed the glass to her left hand. There was not enough time for her to do that, especially lying on her side like she was.
Continuity mistake: When they decide to use the second Pegasus missile, the guy with the glasses says that they still have eight possibilities left. The Admiral tells him to pick one. He is about to pick Delta, then switches to Kappa. In a previous shot that shows the large screen with all of the remaining satellites, when the guy said that there were still eight left, the Kappa satellite is not there.
Continuity mistake: The 2 captains are thrown out of the train into the river under the bridge. Later on, when the shooting starts in the hostage's cars, they're back and one captain is shielding the other.
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.