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Every time I'm around mosquitoes I start thinking about how people made the entirely correct connection between places with a lot of temperate stagnant water and the spread of malaria, but didn't quite connect all the dots - this place has stagnant water, this place has people getting sick with this same illness. Clearly it's the stinky water causing this, maybe it smells bad and the bad air is causing this. It's unhealthy to breathe the outdoor air at night, people who are out at night or don't shutter their windows tightly when the sun goes down are more likely to get sick because the bad air gets in.
The missing middle part was mosquitoes. Mosquitoes breed in standing water, and mosquitoes spread malaria.
I think this kind of thing would make a fun worldbuilding exercise. Have something in your world that does function the way people think it does, but they're completely wrong about why that happens. Or they've gotten the right connection, but backwards.
Holy rites that ward off evil but the Pure Substance is actually just antibacterial. Birds whose call is an omen of an approaching dragon, but these birds actually just have some symbiotic relationship with them. Half-elves that seem predestined to turn to dabbling with dark and lethal magic, but actually they just have a stronger tolerance of The Thing That Kills You due to hybrid vigour. Everyone knows that tigers never attack holy women because of a pact between their gods, but actually it's because a tiger is an ambush predator and the priestesses' headwear vaguely resembles a human face from the back, and the tigers can't quite tell whether she's facing away or towards them.