You say 'There wasn't ever "a big sea full of fish and anyone could just do whatever they want".' But to the contrary, that's basically always been the case. Fishing boats were limited by technology and the size of their local markets, but once those limitations disappeared because of inevitable technological progress, then that's exactly what happened. And we see this happening especially with Chinese overfishing today.
You're claiming that supposed "systems of control" existed in the first place and then were attacked, but that seems entirely counterfactual to me. There was no system of control for a problem that technological progress hadn't created yet -- humans don't see that far enough into the future. And if four countries that border a sea want to limit fishing but a fifth one says I'm going to overfish as much as I want, well then what do you think is going to happen?
I don't see what benefit there is in attacking the concept of tragedy of the commons. It's not some kind of fatalistic viewpoint of what must happen (which you seem to be claiming -- "that people/communities cannot manage resources held in common"), but rather a warning of what will happen when resources aren't properly managed. Claiming the tragedy doesn't exist seems like it would only benefit the people who want to to exploit our shared resources. By recognizing its validity, we can do our best to create and improve systems of management (especially international systems) to prevent the tragedies from occurring.