When the protagonists arrive on Infant Island, the skeleton of a turtle is seen in the background where it appears move slightly. This is often misunderstood to be an error but it's actually an intentional choice, inspired by the Italian documentary A Dog's Life (1962), which showcased the decomposed remains of a turtle that swayed in the wind. Many fans however took it further, pointing out that it appeared to blink suggesting it was indeed a living, albeit disfigured, creature. The creature eventually was nicknamed "Skeleturtle" and developed a cult following. It would make a cameo in a Godzilla comic and Toho themselves would sell merchandise of the creature, cementing its status as an actual kaiju with it's official name being translated to "Mystery Bones of Infant Island".
When the sequence of Godzilla being firebombed was being shot, during one of the takes the flaming liquid splashed up onto Godzilla's head. The fuel quickly burned away and the flames went out. Inside the suit, performer Haruo Nakajima was unaware of the accident, since the head of the suit is well above Nakajima's own head. Godzilla's head aflame became an unplanned bonus to the effects shot and it was included in the final cut.
This is noted for being the final film in the Showa Era where Godzilla is explicitly depicted as a malevolent figure, as the subsequent film would begin transitioning Godzilla's role from a villainous one into a more heroic one. Japanese film historian Yoshikuni Igarashi noted that Godzilla's change occurred alongside those within Japanese society as memories of the WWII were fading, writing, "In 1960s Japan, a place overflowing with optimism inspired by economic growth, the darkness that prevailed in the mid-50s vanished from the screen and Japanese society, Godzilla tamed and transformed into the guardian of postwar Japan's prosperity."
The famous scene where Godzilla destroys the castle in Nagoya actually had to be filmed several times, and the castle had to be built twice. To make the castle fall correctly, two men are sitting behind pushing it with long sticks. The first time the scene was shot, the two men pushed too soon, and the castle collapsed before Godzilla even touched it. The miniature castle then had to be rebuilt. The second time the opposite problem happened, and the two men missed their cue. A second take had to be done with Godzilla clawing away at it as the two men push it over from behind. The moment where Godzilla's foot slides on the ledge (causing him to fall into the castle) has been thought by many to be an accident. According to suit actor Haruo Nakajima, the fall was actually scripted that way and done on purpose.
The adult Mothra is this film is the same creature that was featured in the finale of Mothra (1961), which this film is a sequel to.