I had a male who did this as well. What I did was each time I filled the bowl with food, I would pull the bully out and hold him while all the other rats would go eat. I held him near the cage so he could hear and smell what was going on. After about 5 to 10 minutes, I would put him in another section of the cage with a handful of blocks just for him. I always put blocks in multiple places in the cage, even hiding them in some places so it gave them a chance to use their foraging capabilities and their sense of smell. Each time my bully was being a jerk, I would pull him out of the cage and put him into a small care, very tiny cage with nothing in it. No food, no water, no toys, no bedding. I kept him in there for no more than 10 minutes each time. After about 2 weeks to a month of this, he completely stopped.
Your babies will soon grow up and learn what they can and can't do. I'm sure they will understand the rules of the cage soon enough and be ok with it.