The supernatural referred to anything that appeared to transcend the laws of nature.
In 2268, when the Enterprise traveled to Kalandan outpost, Captain James T. Kirk referred to it as a ghost planet, due to the unusual phenomenon associated with it, as it was too young of a world to have life on it. Spock, however, disagreed, saying he didn't see anything supernatural about the planet, despite his inability to give a scientific explanation. (TOS: "That Which Survives")
In 2269, when Lucien transported Kirk, Spock, and McCoy to Megas-Tu, they initially found themselves to be of a strange ghost-like form, which was unsettling to them, and because of this, Lucien used his magic to make them appear in a form more to their liking, as they would look in their own universe, but he told them holding them together like that wasn't even natural. (TAS: "The Magicks of Megas-Tu")