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' 1960 Mercedes 220 S is crushed by the landslide, it changes to a 1963 Toyopet Tiara for the shot of Malmess extracting himself from the wreck.
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 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.
Crew or equipment visible
During one of the scenes in which the pick axes and rocks are being attracted to Ghidorah's meteor, a hand is seen throwing the last rock.
The Rodan head puppet used for close-ups does not match the full-size Rodan suit's head. The puppet head has bigger eyes, and a smaller beak.
The buses in which the frightened crowd tries to escape from Rodan wobble around like small models as they drive through the parking lot.
As Ghidorah is destroying buildings, the windows of one fly into the air intact, revealing that it's made out of see-through plastic. Real glass would have shattered, but the window remains intact.