I think that they cancel each other out. I mean, the Foundation has controlled countless society destroying threats, but before the Foundation not one of them managed to kill us all. I think this is because, yeah, the anomalous dominated the world, and it could crush all normal life, but, I think that whenever one decides to go on a species destroying rampage they will eventually come upon another that cancels out there effect. Super Virus come across inanimate objects that assimilate all biological tissue, Kaiju sized behemoths come upon incorporeal creatures that they have no way of hurting, anomalous events are dispersed by deity like beings. So, every patch of the earth had its own monsters, and only now are we realising the full extent of them.
But, eventually they declined. Probably through human influence, now we have random anomalous objects scattered over great distances. The order was broken, and only now are the monsters revealing the full extent of their power.