This is not that different than ordinary laws in normal civil society. Sometimes a death is murder. Sometimes it is a lesser charge like manslaughter. Other times it isn't a crime at all (for example if the person was killed in self-defense). What type of crime it is depends on the facts at hand.
Similarly, carpet bombing a densely populated area would be an obvious war crime. However, targeted bombing (which is what israel claims to be doing), maybe - maybe not. It depends on things like how good the targeting is, what is the expected collateral damage, what is the expected military benefit.
Justice happens when everyone is held to the same standard of whatever the law is at the time the offense was comitted and evidence is used to demonstrate that the perpetrator's actions met the elements of the crime. Yes, those types of requirements are hard sometimes, but that is what separates justice from vengence.