I think you might be onto something there. Some time ago, I read something about a chemical (I think it could have been a drug to prevent miscarriages, but another part of my brain insists it was a commonly used pesticide, sorry, my memory is chaotic) that gave girl babies an increased risk for cancer of the reproductive organs, and changed some sexual characteristics in boy babies (distance between anus and testicles or something) and increased the rate of transsexuality.
However, I think boys affected by such drugs would be old-fashioned transsexual, and actually want to have a female body, not insist that their penis is female.
It is possible the whole issue is just drowned by the wave of transgenderism. If there was no transgender trend, a steep rise in transsexuals would be noticed, whereas as things are, no clear distinction is made between those who feel genuinely dysphoric about their bodies from birth, those where dysphoria only develops over time (girls who hate their bodies after puberty) and those that don't have any dysphoria at all (the infamous transwoman with an allegedly female penis)