I’m an atheist through and through, but the one thing I’m unsure about is consciousness.
We basically made zero progress in figuring out what it physically is, how to test for it or how it is created, despite every single one of us experiencing it first-hand every day of our lives. That might be a sign that our physical understanding of reality is just not equipped to deal with this question.
On the other hand, if it has physical consequences then it must measurably interact with the physical world, and maybe it emerges from the complex interactions in the brain somehow. I personally just cannot imagine how the thing I’m subjectively experiencing as myself could ever arise from “dead” atoms and molecules.