Soooooooooooo......
The one commando, Doc, didn't make it onboard the plane......why?
"You asked me to find the son of a bitch, sir. I never thought the son of a bitch would be you."
Seriously.
There simply wasn't enough time for him, or the other commando - older guy, to get onboard.
If they had waited any longer than they did then everybody would have died.
They had no choice but to leave some men behind to die in the stealth plane.
The commandos knew the score / deal. Sacrifice themselves to save hundreds of innocent civilians/ passengers.