I do not know. Perhaps, and this is conjecture, there are reasons for those apparently flawed parts that we just don't know, but that the omniscient designer does. There are many things that human beings have designed that can cause major problems when not used properly or when used without understanding. When they are used as designed, they work as intended. Maybe the problem is not the design, but operator error. I may have my cranium inserted in a receptacle not designed for it, but when you're talking about omniscient, all powerful beings, I'm guessing that the aforementioned being or beings would have more of a clue than we do. That said, if that being or beings can't be proven to exist to the skeptical, then my whole conjecture doesn't get very far.