The stars are missing from most shots during Moguera's first clash with SpaceGodzilla in outer space.
While Spacegodzilla is telepathically levitating Little Godzilla, strings holding Little Godzilla can be seen.
In some of Godzilla's rampaging scenes, some of the fleeing extras are smiling and a lot of the people and vehicles in the background are calmly going about their daily lives.
The end of Godzilla's tail breaks off when he dives under the sea at one point in the film and is briefly visible.
After Godzilla comes to Kumamoto, in one shot, part of him isn't visible between the railings on the top of the Kotsu Center Hotel. Instead, you can see the sky backdrop.
During Godzilla's city destruction, in one shot the farther parts of the city are faintly visible and faded, whereas Godzilla, standing even farther, is clearly visible, revealing that he's been added later on into the shot.
Land Moguera is misspelled as "Rand Mogera" on the monitor screen.
At some points in the movie, when Godzilla roars, you hear SpaceGodzilla's roar instead of his own.
It is suggested in the movie that SpaceGodzila was created by G-cells that got to space either attached to Mothra or from Biollante. The theory about Biollante being the source doesn't make sense. In Godzilla vs. King Ghidorah, the movie immediately following Godzilla vs. Biollante, Godzilla's history is effectively rewritten by preventing his creation and replacing him with King Ghidorah. As such, Godzilla's fight with Biollante, and in fact Biollante itself, should no longer exist in history.
When SpaceGodzilla destroys a space station with his crystals, people immediately think that it must have been a giant monster. What lead them to this conclusion, considering the only things they saw were crystalline spikes tearing through the space station?