I don't know; and neither do you, because we weren't there.
What I do know is that the knee-jerk reaction of, "he didn't do anything wrong because it's a war," is wrong--as wrong as would be the knee-jerk reaction of, "he must have done something wrong, he's a soldier," if I had said any such of a stupid thing.
What I suspect is that something was way off, or neither of these lieutenants would be on trial--because other things being equal, the military does tend to take care of its own and to cover its ***.
But something political might've happened, especially in Lt. Pantano's case--and it looks rather as though in the "Lt. L," case going on in San Diego, something damn sure political did happen--the CIA was involved. Here, the whole torture thing is deeply implicated--guy died in Abu Gharib prison, the circumstances involved beating a torturing a helpless prisoner (evil guy, it seems, but a helpless prisoner all the same), and then there the whole, "independent contractor," nonsense.
But we don't know.