Sure. An obvious example is the metaphysics of time. Given how fundamental it is to our understanding of reality – both physical and metaphysical – you’d think physicists would have this one nailed. Nothing could be further from the truth. All the old questions about time still apply, except now it is complicated by three different branches of science which can’t agree with themselves or with each other about the nature of time. One is Relativity – is space-time ontologically real? If so, is it fundamental or does it emerge from something deeper? If it emerges from something deeper, then how does time work at that deeper level? Another is quantum mechanics, in which time appears to be almost completely reversible – that it doesn’t matter whether time goes forwards or backwards, because the laws work either way. This sets up questions about possible retrocausality that nobody previously thought to ask. The third is cosmology, where we have a growing number of anomalies, many of which seem to involve our understanding of the early cosmos, and that demands a theory of “deep time” which currently isn’t available. What does it even mean to talk about the cosmos in the first moments after the big bang? When we observe distant objects with the JWST – some of the very earliest structures that formed after the Big Bang – what are we actually observing? Is it like a “baby photograph” of the early cosmos? Or is it a retrodicted observational surface?
Another example is the Measurement Problem in QM. How do we get from a set of quantum possibilities to a singular observed classical outcome? QM is 100 years old, and we are no closer to answering this question than we were at the beginning. The real problem is the lack of consensus, and this gets worse every time a new interpretation is invented. So there’s a meta-question here: why can’t we figure this out? Why is the situation getting more confusing instead of less?