Which ones? I don't know of settled science that has been found to be false, but maybe I just don't know.
Sometimes a new theory might eclipse another theory - cover all that ground and more, but that doesn't make the prior theory wrong in any way. My new, faster laptop doesn't mean the old one didn't work.
Phlogiston theory is post-Baconian. To me, Bacon was the first to articulate the method of thoughts that characterize good modern science: Observations, theory, prediction, experiments to verify the predictions. So I don't think saying we've thrown out pre-Baconian theories is germane to the conversation.
There is a Wikipedia page for Superseded theories in science. https://en.wikipedia.org/wiki/Superseded_theories_in_science
If that's the best you have, we agree! :)
Richard Feynman said "Science is the belief in the ignorance of experts", and Carl Sagan said the "Science is a way of thinking more than it is a body of knowledge". Both of these point to the reality that our current understanding of the universe is riddled with errors and omissions. We do our best with the data we have, and try to transcend our own prejudices and history.
How much or our current understanding is "just as wrong?": Well, like most things, it's on a continuum, and to some extent a matter of opinion. Was Newtonian mechanics "just as wrong" as Ptolemy, when considering Relativity? I wouldn't say so, but maybe you would. Ptolemy's conception explained almost nothing and glossed over contradicting facts. Newton put mathematics around observations available to him, but named the reality that he had no understanding of how action-at-a-distance happened. "I make no hypothesis".
In fact, astronomers today don't even use a "heliocentric" frame--they use a barycentric frame, i.e., the spatial origin is the barycenter of the solar system. The Sun is of course much closer to the barycenter than any other body, but it's not exactly at it.
At least not for any precise definition of "just as wrong" that would be useful.
There is, today, not a single terrestrial observation in contradiction to GR and QM. We have an incredibly good understanding of the fundamental nature of our reality.
Our understanding is so good that it takes decades of work by brilliant scientists and engineers, to build machines that could show even the slightest evidence of something else going on.
It's easy to overlook how stunning this situation is. It is utterly unprecedented in the history of science.
This does not mean that there are no deeper truths to discover, but Newtonian mechanics does correctly describe how the apple falls, even if it is not the final word.
Example: what if it turned out that time itself had qualities no-one had suspected before? Time is one of those fundamental things in existence that may (or likely will) still reveal some previously unknown aspect. Which in turn would likely affect our perception of all things in existence.
Which means our "primitive" concept of time (and everything in it) would perhaps not be wrong, but incomplete. Or plainly wrong, for that matter.
"All models are wrong, but some are useful" [1]
The validity of Newtonian mechanics didn't change because we discovered relativity just like the equations of motion don't become invalid because there's friction. It's still useful, we're just more familiar with the boundary conditions where it breaks down. It's unlikely we'll ever throw it away because it is the simplest model with a lot of predictive value at low energies.
I don't think getting to the point of throwing anything out is necessary, if (some adequate subset of) humans could even get to the point of seriously wondering if our models and beliefs (across all domains, including those outside of science, particularly those which science sits on top of) contain zero fundamentally important flaws, I believe we would be well on the path to sorting the mess we've made out. Science and engineering are excellent examples of how capable humans are when they really set their minds on trying to understand something.
What we do have in our current physics is a reasonably good understanding of the limitations of our theories: we know that none of them are theories of everything, they all have limited domains of validity, even if for some of them those domains are very wide. That is the key thing that systems like those of Aristotle and Newton did not have.