"Why? They must have had plenty of real criminals, why go after such minor infractions?"

It's a question of desperation more than confusion. He remembers the labs in Raven Rock and can easily imagine how they could have perpetuated, how someone like Dr. Holland or his brother could consolidate their control. Restoring America and building the population up was supposed to change things. It was supposed to result in happy families in quiet and peaceful neighborhoods, Old World democracy and justice, people able to live private lives. That was what he'd always fought for. Vicious tactics are justified to reach that victory, but once the fight was won...things were supposed to change.