Physics (especially classical physics) has the advantage of dealing with things that are both extremely repeatable and consistent, and are just about omnipresent. When a physics model is flawed, you start piling up edge cases that violate our current understanding of physics, until someone comes up with a model that explains most of them while not violating the relatively decent predictive power of the previous models (which obviously have predictive power, since they've been being used to predict things successfully for a while).
For example, Newton laid out classical mechanics. Which very adequately modeled most things moving around in scales we could observe. Except Mercury's orbit was a little fucky. Now, one new model could be that "Classical mechanics works everywhere but on Mercury, where they have different physics", but eventually relativity was postulated, and calculated to predict Mercury's orbit to within our ability to observe it. Rinse, repeat, for things like QM, orbital mechanics, etc, etc.
Heck, there's a pile of inconsistencies in our current models. Neutrinos have mass, the universe's expansion is accelerating, and where's all the antimatter?
