PT-boat weapons followed the targets actually encountered

Were PT and motor torpedo boats misused during the Second World War?

Not fundamentally; their missions changed, and gun armament often suited interdiction and fights with small fast ships better than torpedoes did.

PT and motor torpedo boats were used about as effectively as their difficult circumstances allowed. Their large wartime expansion meant many crews and commanders lacked the peacetime experience available in established ship types. Torpedoes made sense against battleships and cruisers, but guns became more useful when boats performed interdiction or fought destroyers and smaller craft. Hitting a fast, manoeuvring destroyer with a torpedo was extremely difficult, so the weapon fit naturally shifted toward gun power.