Is attacking a military versus civilian target the determining factor of tribunal vs. federal court?

This question is posed due to a couple responders who answered a recent question of mine, and I find that perspective interesting. If that is the case, and the attacks of 9/11, who were masterminded by KSM, were not an act of war but simply m murder, how do we factor in that one of their targets was the Pentagon, which is the beacon of our military in DC? That would constitute a military target, would it not?