Epic fail

This is kind of a bug in the way natural selection works. As bad recessive genes become rare, individuals who have two copies of them and so express the gene become rare squared, and the selection pressure against the damaged gene dwindles. We end up all carrying around damaged genes, but generally all have different selections, so get working versions from our other parent. But breed with someone too closely related there is far more chance that the offspring will get two bad copies of something.

Maybe Darwin married his first cousin as an experiment.

Incidently, being a carrier of a recessive disease gene can sometimes offer a benefit (as well as induce some symptoms). For example cystic fibrosis is much more prevelent in people with northern european decent than african/asian (around 1/2,500 versus 1/90,000). This is thought to reflect an evolutionary benefit in being a carrier (1/25 of UK population), such as resistence to Typhiod.

The bad genes aren't all necessarily just redundant code, they can still be selected.