The theory of evolution by natural selection is now scientific orthodoxy, but when it was unveiled it caused a storm of controversy, from fellow scientists as well as religious people. They criticised it for being short on evidence and long on assertion and Darwin, being the honest scientist that he was, agreed with them. He knew that his theory was riddled with 'difficulties', but he entrusted future generations to complete his work and prove the essential truth of his vision, which is what scientists have been doing for the past 150 years.
While Darwin knew of inefficient anatomical features of humans and other animals, he didn't consider these a distinct category of evidence for natural selection. Explore ad hoc body designs - from our imperfect eyes and sexual anatomy, to the bizarre faces of flounders and the false thumbs of pandas. Each adaptation shows evolution devising a solution that is "good enough," even if it's not ideal.