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Physics has, since it's inception, suffered from issues of epistemology and semantics. That is, what can be 'considered in the realm of inquiry' and what is meant by the words and definitions used to explicate phenomena.
The article from Aeon covers some of the paradoxes and philosophical problems which continue to haunt physics.
https://aeon.co/essays/the-paradoxes-that-sit-at-the-very-core-of-physics