The bloody mess we're seeing in Iraq today is typical for the end of any war.
World War II ended in Europe in May of 1945. But the fighting, on several fronts, lasted for years. Italians battled Yugoslavs around Trieste; Greeks and Turks fought their own; there was a practical mini civil war in France against collaborators; French colonial forces found themselves at war in Indochina; the denazification of Germany was sometimes bloody (much like what we're seeing in Iraq today); and more. "It's a little-known fact, Diane," that partisans in the newly-annexed western Ukraine kept fighting against their Soviet overlords well into the '50s.
Probably the only reason the occupation of Japan went so smoothly is that the Emperor had commanded his people not to fight