Goofs

Due to stock footage from the previous movie being used, MechaGodzilla's look keeps changing. Look at the chest and the hands - these were redesigned for this movie, yet the revert to their older look in closeups.

The aliens in this movie are said to belong to the same race as the ape-like aliens from the previous film, but they look completely different. Previously, when being injured or killed, the aliens' human disguises faded away by themselves, revealing that they really look like apes. In this movie, the aliens tear their human masks off manually, revealing freakish, distorted, human-like faces underneath.

Godzilla's appearance drastically changes when he returns to the ocean, as a different suit was used for this scene, namely MechaGodzilla's fake Godzilla disguise from the last movie.

The alien leader walks into MechaGodzilla's head through a rectangular door that only exists in this one shot.

While Godzilla tries unsuccessfully to stop Mechagodzilla from destroying the planes firing at them, he is standing. After a shot of the planes being destroyed, Godzilla is down again being kicked by Titanosaurus.

The sign (in English) in front of the Ocean Development Laboratory is misspelled "Laboratry".

In several shots when Godzilla is being blown aside by an explosion, kicked across the landscape, or flung high into the air by his upper lip, it is obvious that he is actually an empty suit, because he looks inexplicably thin.

As Godzilla sends Mechagodzilla flying in his final scene, Mechagodzilla also seems to be represented by an empty suit here. His hands wobble around and appear to be attached via thin rubber or strings or the like to his arms, rather than being held in place by an actor inside the suit.

Titanosaurus' neck sometimes bends too much, indicating that it is not supported firmly enough from the inside. Such movements would cause the spine of the animal to break.

When the recently malfunctioned Mechagodzilla is hurled at a hole in the ground, the strings holding him up are visible.

When Titanosaurus kicks Godzilla out of the city, Godzilla's body flies in a straight line, then does in an upward curve over a hill, then begins falling again.

When MechaGodzilla opens fire on Godzilla, who's lying in a ditch, it first shows Godzilla in the pit, then immediately jumpcuts to the same scene from another angle.

When Godzilla roars for a last time, his mouth doesn't move.

At about 45 minutes into the film, Titanosaurus is being bombarded by the air force. The electrical wiring and the pyrotechnic explosives and clearly visible along both sides of his neck.

In the previous movie, the aliens had to find and kidnap a professor to help them. However, this movie establishes that they have been working together with another scientist for several years, thereby retroactively causing a plot hole between the two films.

According to the backstory, prof. Mafune was banished from the scientific community because he claimed to have discovered dinosaurs and found a way to control them. This happened 15-20 years prior to the movie's plot, but by then, several dinosaurs and other strange monsters, including two Godzillas, have wreaked havoc in Japan, so why would the discovery of yet another giant dinosaur be dismissed as nonsense? Further, since they have caused so much destruction, it would make more sense to let Mafune continue in his studies to be able to control them, rather than banish him.

Prof. Mafune doesn't initially learn that the people helping him are aliens in disguise. But if he thought they were human, why did he continue to harbor hatred toward humans? As far as he knew, he was being helped by a group of humans, so that should have eased his hatred.

When Katsura speaks of several past monsters (with a montage appearing around her), she names one as Radon. That's the Japanese name for the monster American's know only as Rodan.