Surprised that no one's
brought up the trope yet- it's at least tangentially related.
In most narratives, the watchword for the common folk is 'strength in numbers'. Or, to put it another way, 'quantity has a quality all its own'. Generally speaking, there are gonna be a whole bloody lot more of the common folk than the super-types (whether 'super-human', super-natural' or whatever), and humans, no matter how ordinary, are terrifyingly good at figuring out how to kill things.
Even Saitama, for all his game-breaking power, isn't outside the realm of possibility for mundanes to put down; at least, not entirely. It's implied pretty strongly that he still needs to breathe (cf. when he gets blasted to the moon) and he still sleeps, whether he has any actual need to do so or not. Put some decent surveillance on him (as far as I can tell, his travel speeds are still observable), sneak in and remove his CO2 detectors, turn the gas on, and leave. Even if he's totally immune to poison (which is certainly possible, given that this is Saitama), not having any breatheable air in his apartment while he's asleep is gonna do him in.
Muggles also talk to one another- in a modern setting, the level of problem-solving available on any subject that you can get enough people interested is ludicrous. Almost nothing that you can get enough (bored) people looking at will remain any kind of a secret, at least not for very long.
So... what can muggles do? Piss them off enough, or get them curious enough, and there's almost nothing they can't kill, almost no secret they can't discover.
... all of this with the caveat that yeah, there are power levels beyond what mundanes can have any perceptible effect on.