but each time they point and say there, that's a monad! They are proven wrong.

You simply don't know what you're talking about. I sincerely think you don't even know what you don't know. The conception of the monad has literally nothing to do with what you're talking about here. Not once in the history of philosophy has there been an event such as what you're describing, nor does it have any relation to the actual relation between science and philosophy.

Philosophers, in this context, have not been looking at explanations of new scientific discoveries, and then calling whatever the new discovery is "a monad", before being proven wrong by something even more fundamental. The conception of a monad is something which is far more fundamental, as a matter of accounting for the ontology of material existence itself, than anything you could possibly bring up in terms of atoms, protons, electrons, quarks, etc.

You've simply either completely missed the point, or you never knew anything about this topic at all until about half an hour before I started typing this comment.