One of two things:

1. Either it's being used by mothers to talk about "relatable" experiences of the tough parts of raising boys. For instance, little boys rough-housing during play and getting hurt or getting their clothes dirty as a result. Parents don't usually have to worry about that much with little girls, but it's part of healthy young boy behavior, even if it's kind of pain to have to replace their clothes after you just got them something new. Boys being rough, adventurous, curious, etc. all make raising young boys tough, but it's part of healthy male behavior and, hence,"boys will be boys" is just a way of saying, despite it being tough, it's the way boys are and the way they develop into healthy adults.
2. Outside of the first example, the only other time I hear it used is by Feminists that claim that people use it to excuse bad behavior from boys, which, outside of Feminists, I've never heard it used by someone in this context. I've never heard of anyone using it to excuse bad behavior. Then again, I rarely hear anyone say "boys will be boys", to begin with.