What religion are you? Christianity says he's omnipotent. "God has no control..." is totally wrong. He has total power over everything. You could argue that he chooses not to use it, but if you're Christian and believe in the Bible, he has the power to do anything. He created the world and has total knowledge over what that allowed for, and he created those possibilities. If he didn't want intersex people he wouldn't have designed his creation with that "flaw". This is pretty basic stuff man. Go pick up your Bible.

Also, again, intersex is not gender or anything else. It's just one of many conditions of being that humans have.