GR is a theory expressed in terms of maths. The singularities it produces are mathematical singularities.
That said, most physicists believe that the singularities are really just the mathematics throwing up its hands and saying "I dunno". That is, we believe that somewhere between the regimes we have tested and the singularity GR stops being an accurate model of reality. And we hope that a future theory of (quantum?) gravity won't include singularities.