What does that have to do with anything? How rare something is determines whether it's an illness? Again, you are speaking in ignorance.
Why? Why is it such a problem?
You are conflating sex and gender. Gender is psychosocial. Sex is biological. Intersex individuals exist, which is more complex than your simplistic understanding of sex chromosomes. Gender, although related, is distinct.
The fact is, if you want to deal in facts, that for millennia, across time and culture, there have been individuals who do not conform to the gender norms of their culture, or are psychologically more aligned with the opposite gender, or a blend of the two. In some cultures, even non-Western ones, these people have been identified as being a third gender, centuries ago. Whatever label we want to put on these individuals, the moral of the story is that both our sex and gender binaries are overly simplistic and do not describe all individuals. And there is nothing "wrong" with individuals who don't conform to our binary constructs of how males or females are "supposed" to act or identify or be. They are simply different. What is so hard to accept about that?