Rape happens everywhere and anywhere in peacetime and war. In mine point of view it is always a crime. But like with every crime one must look at the circumstances. Not so very long ago rape (and plundering) was considered a reward for the victorious soldiers. I think the British, and certain under the command of Wellington, were the first to punish this behaviour.
Another point to think about is how long were these soldiers on the battlefield? The longer they are and the more ferocious the combat the more likely those soldiers will rape someone. Think like I wonna f..k someone before I get killed. Soldiers are trained for combat not to be a gentleman, although a lot of (mostly leftwing) politicians and activists ask the impossible from them.
Did you know that Napoleon had prostitutes following his army?
For a commander the loss of a soldier is bad news. Wether he got killed or send away because of a rape, on paper it is the same: his force is reduced. So I can understand that commanders cover up rape crimes. They have to focus on their mission and are always short of soldiers and weapons.