The suspected "monsters" are not necessarily space aliens, right? People are suspecting the mischief is done by ghosts or witches or devils, but the villains turn out to be mortal human beings?

If the monsters are not real, then the story with that plot is not necessarily sci-fi, and therefore not necessarily on topic here?

@user1411 yep, exactly - they can be perceived to be any sort of non-human 'monster'. I suppose it may not be necessarily, but all examples I've encountered have been episodes within explicitly sci-fi/fantasy series, and I imagine the story would be 'framed' in a sci-fi way up until the big reveal.

Well, any episode of Scooby-Doo fits...

@Raj The trope I linked is much more general than what I meant, but it does include some of the examples I listed (Torchwood, Supernatural), so I added it as there might be some earlier relevant ones amongst it. I like your example (as with the one user1411 posted, Sentry) - it's not the exact same narrative beats (two 'species', each thinks the other is the real monster and they're only acting in self defense; as opposed to a clear an-/pro-tagonist setup & they're all the same 'species'), but it's pretty close thematically.

This somewhat fits to "the Village" as well.

Well's "The Time Machine" could possibly be argued

I believe I've also seen it used in old EC Sci-Fi comic titles.

Does it have to be sci-fi specifically? I'm pretty sure there are dozens of fairy tales that fit this description.

@BlueRaja-DannyPflughoeft sci-fi or fantasy, I don't mind - it's just all the examples I was familiar with were from sci-fi series.

So you're talking about things like Monsters Inc. and Smallfoot?

The Hound of the Baskervilles might fit, if one could find a way to look at it as SF or fantasy....

Read as far as "Countrycide" and immediately thought 'OH! Like "Home' and 'The Benders'!" before reading that of course those were the next two examples haha

I'm also curious to know the first example of the more specific trope of: "Series that consistantly deals with mystical/inhuman threats has an episode where the twist is that the threat is in fact mundane/human in nature." All three of the episodes given are backed by the expectation of an alien/monstrous threat due to the context of the rest of the show. I'm trying to think of other examples as I'm sure there are a few

Does Frankenstein count?

Does the 5th wave count?

Not sure if that counts, but in Beowulf (written around AD 700–1000), the monster Grendel is descent from the biblical Cain.