So it is far from clear that, even if the 9/11 attacks had been carried out by uniformed military, these would have been war crimes. It is, however, beyond doubt a violation of U.S. and New York State criminal law for civilians to attack skyscrapers with airplanes.
The internal justification for area bombing either espoused a view that civilians were collateral damage to attacks on the industrial war machine or that in modern warfare, the civilian/combatant distinction was not viable or important. In some cases, bombing of civilians was, ironically, presented as humanitarian and in keeping with the larger goals of the law of war, in that collapse of the enemy could be precipitated faster, and at a lower cost in human life overall, if civilian morale could be broken from the skies.