This is where I see an odd tension between my quite-left-wing views on gender (at least, fitting with a portion of the left) and the views generally promoted by this portion of the LGBT universe. Since I don't really believe in the gender binary, it's quite strange to even talk about "correct" or "incorrect" genitals, except perhaps as shorthand for "physical sex characteristics that are in greater/lesser conformance to socially constructed gender norms for that sex". I can certainly see why someone who felt they better matched the A gender role but was born with B sex characteristics would want to switch, but I see that as more of a problem with rigid gender roles than with anything else.
It even a little uncomfortably feels like it perpetuates traditional gender/sex views, that there's something incorrect about someone with particular physical characteristics not fitting a particular gender role--- and that they need to correct it by changing their physical characteristics to match. That's certainly a choice people can legitimately make, but phrasing it as correct/incorrect comes uncomforatbly close to stigmatizing people who don't match traditional gender/sex conformance and yet don't feel that there's anything about that that needs "correcting".
(I agree in either case on calling people by whatever gender pronoun they prefer, though.)