How can that be a problem? That's like saying the problem with the evolution theory is that everything that 'is' evolved. There are only two logical theories: evolution and creation. One requires everything to have evolved the other requires that everything is created.I don't see that as a problem at all. Or maybe, that is the problem with both, and the difficulty in proving either of them.
According to evolution, fish evolved but pebbles did not. According to creation, both were created.
How are those alternatives? I believe that God created everything, and that evolution is the way He created living things.