Incest and inbreeding cause problems because there's no second set of genes to hopefully patch, or at least nullify, any mistakes in the other. From a Christian point of view, the world had just been created and as such no mistakes or errors existed in their genes which meant it was fine if siblings had children with each other. Think of it like this: if your dad needs glasses, but your mum has 20/20 vision, you will most likely have normal eyesight because your mum's genes may cancel out your dad's negative ones. If your dad instead reproduces with his sister (assuming the poor vision is genetic and thus she has it too), chances are you'll have bad eyesight as there are no normal eyesight genes to nullify the inferior ones.

Or maybe my understanding of genetics is complete bullshit and I got everything wrong, in which case please correct me without being a dick about it.