How many actual scientific theories have been outright debunked. I don't count pseudoscientific bafflegab like phrenology or Ptolemaic cosmology as being science. I'm talking about out and out scientific theories posited under something approaching the methodological naturalism that evolved out of the Enlightenment.
Take Newtonian mechanics. While in the strictest terms it isn't right, but for most non-relativistic purposes (like building bridges or getting a probe into orbit around Saturn) it works just fine. In other words, Newtonian physics was never falsified so much as subsumed into relativity, and become a useful non-relativistic simplification.
A few theories that I can think of that were outright falsified would be cosmological theories like steady state theory, or some pre-plate tectonics geological theories. The ether theory, which had a brief reign could be classified in this category, but my understanding is even by 19th century physics it was highly problematic. Some of the softer sciences may have issues as well, though many of these "so-called" theories were often more philosophy and metaphysics than science anyways.
The bulk of scientific theories may get modified or subsumed into larger theories but never get outright falsified or debunked. Generally speaking, to become a theory means that a helluva lot of work and observation has gone into it. That isn't to say that any given theory might be not be wrong, but still I'd say it's a lot less likely.