Procreation and the root of evil share the same source. Both draw their life from the initial phrase of creation, בראשית. This phrase is referred to as a sealed phrase, but we aren't going to get into why, suffice it to say the answer may be beyond our ability to understand. (Likkutei Halachot Hilchot Kibud Av:4)
It is known that procreation creates a child who is imbued with an animal soul, which includes at least some small part of evil. The Godly (totally good) soul only comes later, at maturation, the age of mitzwoth. (bar/mat mitzwah)
What I'd like to focus on is an interesting tangent: The initial creation of the world involved (at least the potential for) evil, as Rebbe Nachman just explained. Shabbath, the essence of good and all blessing, the perfection of creation, was only created on the seventh day.
To me it's another striking example of how perfect HaShem's world is that the microcosm so perfectly mirrors the macrocosm, a child is created initially with a soul partially evil, and the perfection, the completion of the child only comes about at thirteen (twelve for women) years of age.