Because *contrary to popular male belief* women do not select a man by the size of his penis alone.
A micropenis is well able to impregnate a woman.
But even more: evolution isn’t that precise. Genetics are convoluted and complicated. As a made up example imagine gene A makes you immune to malaria, gene B makes your eyesight fantastic, but having A and B together makes you have no penis at all. Those genes would still be somewhat competetive, because people who only have 1 of them have an advantage and pass the genes on, and women can savely carry AB without issues.
I.E. there is no single-purpose-micropenis-gene.
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