Many of them. While historically the life of the peasantry (and pastoralists and hunter-gatherers) was stereotypically 'nasty, brutish, and short,' war activities were often carefully circumscribed and oriented around set piece battles. The disregard for such conventions was part of why figures like Attila the Hun, Genghis Khan, and Tamuslane were so reviled.

The anthropology of war is a lot more complicated than most people appreciate, because much of our mental imagery on historical warfare comes from movies and other fictional narratives. John Keegan's War in Human History is an accessible starter book on the topic.

I think you'll be hard pressed to find an era in which civilian populations weren't subjected to brutalities during and immediately after conquest of population centers. Battles between armies not touching civilians didn't make war a clean and moral thing.