Well it's not contradictory per se - nothing disproves a god hand-adjusting mutations, for instance. It's just got a lack of evidence which means we should assign it a low probability.
More commonly what I see is that people aren't 100% intellectually honest when they get into it. They don't apply the same rigor to their religious beliefs as they do others. Or they sort of re-interpret or cherry pick themselves around their scriptures to avoid awkward parts. Or they start stepping back and making less powerful claims than their religion traditionally did.
Sometimes they step all the way back into "well what if God is just the laws of physics?". At that point I don't think it's much of a technical discussion and more like, hey, if this comforts someone, and it's not making them make bad decisions (like hurting others based on this belief), well I'm not gonna waste my personal energy arguing.
I mean, so long they aren't arguing that the creator of all spacetime and beyond, of infinite knowledge and capability, cares how we dress or who we sleep with ... eh, fine whatever. Now, people selling water claiming it can cure cancer, that's another story ;).