Megalon can only fire one beam, but in certain shots during the city destruction, multiple beams are seen. This is because these shots have been taken from movies featuring the three-headed monster King Ghidirah firing beams from his multiple heads.
When Godzilla jumps into the water, his appearance changes. This is because this shot is re-used from Godzilla vs. The Sea Monster (1966), which wade produced when the old Godzilla suit was still being used. This film marked the debut of the new suit.
When Jet Jaguar is spinning around and getting dizzy, in the wide shots the Jet Jaguar doll's feet are together and fastened to whatever is spinning him around. In close-ups, the actor in the Jet Jaguar suit is stumbling around like he should be, feet apart.
The car of the main heroes doesn't seem to be pulling any kind of trailer after they flee from the lake, yet the huge water craft that the child had been using at the beginning had to be transported somehow.
One of the nude pinups on the rear window of the truck hauling the container changes between scenes.
One character claims Easter Island is uninhabited. Though its population had decreased to a few hundred by 1966 (and is now about 8000), it has been continuously inhabited for centuries.
When Godzilla is bouncing Megalon up and down, the Megalon suit is empty (the legs bend and collapse, showing no one is inside the suit).
At the end of the film, Jet Jaguar walks away from the two young men and the kid, who run after him. Just before they catch up with him, there is a shot in which Jet Jaguar and the three others are standing still, then begin moving again. Obviously the actors were waiting for their cue. Although this goof was fixed in most later video versions, the recent German DVD edition still has it.
In one of the closeup shots of Megalon's arm when it is fighting with planes, it is actually the arm of another monster, Gigan, stock-footage from the previous movie, Godzilla vs. Gigan (1972).
The shot of Megalon spitting what appear to be explosive "rocks" out of its mouth is clearly a repeated shot that's being shown over and over again.
Pistons holding up the fake military vehicles can be seen in one shot, along with the track they're being pulled on.
Shots of the 'nuclear test blast' that affect Monster Island are lifted from "Destroy All Monsters" (when the aliens gas Monster Island).
The scene of Gigan landing on a building (with yellow and black stripes) is a scene lifted from "Godzilla vs. Gigan".
The opening scene at the lake was supposed to take place on a warm, probably summer day, but the scene was actually filmed in winter, and you can see the breaths of the characters in the air.
To incapacitate one of the Seatopian agents invading their laboratory, Jakavin and Rokkuchan hurry to a hobby shop, steal a model airplane, build it, and throw it at the agent's head, knocking him out. Why didn't they simply use a rock?
How does Jet Jaguar get dizzy after having spun around if he's a robot?
After having knocked out the Seatopian agent, Jakavin and Rokkuchan run off, leaving the agent at their lab. This makes no sense, they should at least have tried to tie him up or get rid of him through other means. They don't even try to take back the lab.
Both Jet Jaguar and Godzilla are trapped in a ring of fire created by their foes, and they only escape with the help of Jet Jaguar's flight ability. Since Godzilla is near invulnerable and has survived much worse (including being briefly set on fire in the American exclusive scenes of Mothra vs. Godzilla (1964)), he could easily have walked straight across the flames.
If the Seatopians are an ancient people living underground who have never contacted humanity on Earth's surface before, how did they manage to establish connections with the aliens of Space Hunter Nebula M, a civilization far away from Earth?