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The methodology is fine but what generally happens, and you see this time and time again, is for something we don’t understand all that well a couple of things can happen:
1. Some experiment, say, proves that a theory is correct full stop.
2. Increasing amounts of scientific evidence point more and more towards a theory being correct, perhaps with some adjustments to the theory along the way
3. Increasing amounts of evidence point towards current theory being wrong or at least inadequate. This is the point, generally, where theory undergoes a fundamental change. People recognize that the theory is inadequate, but have no acceptable theory to replace it (there may be several contemporaneous competing theories). It doesn’t mean that science is ‘wrong’ per se, but that we’re struggling to make sense of the data we have. At some point, hopefully, a new theory emerges that makes all of the previous data make sense (a good recent example of this is the theory of plate tectonics).
What doesn’t happen these days is that suddenly some piece of evidence magically shows up that says the theories everyone has been working with are wrong. People often like to point to examples from hundreds of years ago as if this is relevant today. There are enough scientists working on problems today that if a theory is somehow deficient and doesn’t match the data all of the scientists will know about it and will be working to resolve issues.
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