I'm not sure if this is a thing, but I've got three examples, so I'm giving it a shot.
In a fantasy story, some supernatural event occurs, and its effects are described. The characters don't notice, not having access to modern science, but the effects resemble a thing that actually happens in the real world and has (is believed in the real world to have) a non-supernatural explanation.
It's not a case of "this is a natural occurrence that the characters just think is supernatural"; these are stories where the supernatural really does exist.
- In Soldier of the Mist, the protagonist has been cursed by one of the gods to not be able to remember more than a day into the past. He also has a head wound that would have a modern doctor suspicious of post-traumatic amnesia.
- In Odd and the Frost Giants by Neil Gaiman, there's a bit where Odd needs to find a rainbow, so he goes to a waterfall where he's often seen a rainbow in the water. It's winter and the waterfall is frozen, but he figures that if the rainbow was in the water when it froze it's in the ice now, so he cuts out a chunk of ice, holds it up to the sunlight, and gets his rainbow. It's mentioned in passing that the chunk of ice is the shape of a triangular prism.
- In The Curse Of Chalion, the protagonist is afflicted with a tumor that is attributed to him having a demon trapped inside him. He really does have a demon trapped inside him, but that aside the description of the tumor is in accord with medical science; even the doctor's anecdote about a tumor that started developing its own body parts has a basis in fact.