When Rodan flies out of Mt. Aso, you hear Godzilla's roar instead of Rodan's, and also a small clip of the sound King Ghidorah makes. Later, when he confronts Godzilla, he screeches in Godzilla's voice again.
When the assassins' car gets crushed under the rubble, the windows of the car model snap and bend, but remain in one piece. When the camera cuts to the real car with the actors in it, the windows are smashed to pieces.
When Godzilla and Rodan are throwing boulders at each other, the size of the boulders change size from shot to shot. When Godzilla is throwing the boulders, they are fairly large sized. When Rodan is volleying the boulders back, they are much smaller in size.
When Malmess is finally killed, he literally catches the (obviously very-light-weight) boulder that knocks him from his sniper's perch, actually raising it up an inch or two as he topples backward off the cliff with it.