Two of the more famous are General George Patton (World War II) and General Douglas MacArthur (Korea). Lincoln struggled with military officers who got their mouths ahead of their judgment.
Now, there is another. Gen. Stanley McChrystal's sins are not yet clearly known, but he has been recalled to the United States from Afghanistan to explain his words of criticism of the war effort and of his superiors.
This is really not a close call. The Constitution instructs us that the President is the Commander-in-Chief. No matter how talented or untalented the President may be in making war, he is nevertheless the guy. This notion of civilian control of the military is not novel to the United States. Democracy probably cannot survive without it.
Presumably, McChrystal will be punished. He, himself, would expect it.