Law of Large Numbers
The thing about something like this story of a soldier using the Koran for target practice is that it really sets into relief how audacious the goals of counterinsurgency theorists are for what U.S. military conduct could really be like. In the annals of wartime abuses, Koran-shooting is extremely stupid but also really not that bad compared to, say, massacre or pillage or torture. And it's so obviously dumb that, clearly, the chain of command was not sending tacit "everyone shoot Korans" messages down the line. And yet it's still really dumb and counterproductive.
Now consider that our deployment in Iraq has involved upwards of 200,000 soldiers at one time or another. I'd just be phenomenally hard to get a group of people that large together that didn't include any people who sometimes make the occasional idiotic blunder. Indeed, it'd be hard to get a group of people that large (about the population of Reno, Nevada) together that didn't include a few serious bad apples -- murders and rapists and the like. And historically speaking, while good discipline has always been an asset in war, nobody's won wars by having perfect discipline. But the prescriptions for successful counterinsurgency oftentimes seem to me to suggest that we really do need perfect or near-perfect discipline to succeed, and I just don't think that's realistic.