The fact alone that their minds don't match with their bodies definitely means that there is something wrong with their brains.
Just like Intersex people who have physical defects as a result of their genetic disorder. Just as simple as that.
Why do you define that as "defective"? That there is only one "correct" way?
Among humans, there is a huge diversity of sexual development. Sex and gender are complicated; many elements go into their making. The following pieces are all needed in the development/construction of complete femaleness or maleness:
Sex chromosomes – xx for a female, xy for a male
Primary sex characteristics – vagina, ovaries and uterus for a female, penis and testes for a male
Brain Sex – not masculinized for a female, masculinized for a male
Gender Identity – “woman” for a female, “man” for a male
Gender Expression – “feminine” for a female, “masculine” for a male
Hormones and secondary sexual characteristics – high estrogen and progesterone for a female, high testosterone for a male
At any point in the development process, one of these elements might swerve from the norm. A difference at any of these levels creates some form of “gender variance.” This applies to sexualities as well which are separate from gender.
Also, for each of these different sexually dimorphic traits, some people’s anatomies will fall “in between” or “outside of” what most people consider to be standard for female or male.
As one example, some people with androgen insensitivity have XY chromosomes, internal testes, and external female genitalia. Traits, including hormone levels, can also vary widely both within and across sexes. But people who fall outside of what’s considered normal face discrimination. Take South African runner Caster Semenya, who was recently the subject of a ruling that ordered her to lower her naturally high testosterone levels to compete with other female runners — even though studies have shown that because testosterone levels are so highly variable, there’s overlap between the natural testosterone levels of men and women.
See here for more:
https://blogs.scientificamerican.com/voices/stop-using-phony-science-to-justify-transphobia/