The Nanjing Massacre represents a human rights violation precisely because it involved so many civilians who were hapless victims of the war that raged around them. As #2 establishes, even though Japan was at war with China, the way in which so many innocents were abused and killed who were not directly involved in the conflict make this a massive example of a human rights abuse.
Nearly a quarter of a million people, mostly civilians, were killed in the "rape" of Nanjing. This doesn't even factor in all the other crimes that Japanese soldiers committed, including rape itself. If the events at Nanjing weren't war crimes, then the phrase has no meaning.
It's hard to know exactly what you mean by this. Are you asking why we call this an abuse/human rights violation? If so, it is because it involved the killing and raping and other abuse of innocent civilians. The Japanese were at war with China, it is true. But the citizens of Nanjing had not done anything to deserve being treated as they were. Therefore, it was a human rights violation.