There were definitely a bunch of cases of needless (in retrospect) killing, but those were generally mistakes, vs. conscious policy. Given that it is a war zone, and information is imperfect, but that inaction would have its own costs, I haven't seen a lot of cases of seriously bad activity. There is also a gray zone between illegal and unjustified; the few genuinely illegal actions have generally been prosecuted and punished by the military. There were other cases where "bad" things happened which were not illegal, but where the policy was changed as a result to prevent those things.
For instance, due to the incidents such as the madrasa night attack in J-Bad, special operations night raids were sharply limited in 2009 (per GEN McChrystal), and the rules for the use of airstrikes and artillery fires were substantially tightened.
Internal to the military, people don't really cover up this information -- it feels into the process of changing policies. Compared to most companies, lower ranking military people are fairly willing to report bad news up the chain of command (still not perfect, but more so). Almost all of this is "hidden" behind security classification, maybe too much so -- which makes people outside the military assume mistakes are intentional and not being corrected. There is a compelling argument for aggressively declassifying information as quickly as possible, positive or negative.