A classic example was the harvesting of the Blue Whale in the mid 20th century. Near term gain won out over long term valuation of Blue Whales. It was enforced regulations that saved the Blue Whale.
Before you cite the Commons and property ownership as a rebuttal, let me just head off that silliness right now. If a Japanese whaler is able to catch a whale, then clearly they have proclaimed themselves the owner of the whale, whether one considers that legitimate or not. But even so, they obviously only valued the whale as a source of blubber and other various derivative products. Therefore, what we witnessed was a free market valuing the whales at a certain price (for their food and oil products). Is that the correct price?
In the absence of regulation, what would have been the ultimate outcome? Perhaps extinction, especially if the free market worked as you believe it should, that is to say, the price of blue whales rose significantly as their numbers were reduced, for that would've only invited greater effort to hunt the last of the blue whales.