At the end of the film, as Mothra flies back to Infant Island, the large net she is carrying with her feet with the humans inside it is missing.
When Mothra is a matte painting during the Infant Islanders' dance scenes in the film, she looks drastically different from the prop used in the rest of it (for example, the painting's eyes are much larger).
When the Red Bamboo's ship approaches Letchi Island, it is both spraying and covered in yellow liquid, but when it pulls up to the dock, the ship is completely white and no liquid or liquid stains are seen.
In the beginning of the U.S. version of the film, there is a scene supposedly showing Yata's boat being destroyed. Yoshimura is on the boat in this scene, which is called the "Yahlen" and is the boat Yata's brother, Ryota, steals later in the film.
The Shobijin frequently cast no shadows in the film, even when the other Infant Island natives around them do.
The strings holding up the Mothra prop are visible in certain shots.
Before Godzilla tears off Ebirah's claws, you can very clearly see the head of the suit actor inside the Godzilla suit through the big holes in the suit's neck.
Black lines running down the sky backdrop are visible in some scenes.
The strings holding up various parts of the monsters, such as Ebirah's claws, are visible in some scenes.
There is a shot in the film of the control panel inside the Red Bamboo's patrol boat. In it, the left button misspells "Ahead" as "Ahed".
At the end of the film when Godzilla gets ready to escape from the island before it is destroyed in a nuclear explosion, you can see the suit actor's eyes in the suit as Godzilla rears back to jump off a cliff and into the ocean.
Godzilla gets awakened by electricity (lightning) earlier in the film, but later, when he runs into the electric wires surrounding the Red Bamboo's base, he recoils as if the current has hurt him.