Are your chicks in a run along side but separated from the main flock?
I am editing this because I just re-read your comment... When chicks leave the brooder they don't immediately ever go right into the flock, you really need to set up a safe zone until the chicks are a bit older and the adults get used to them being a part of their everyday life... We built a small coop and run next to the main coop, it is separated by chicken wire, that way babies and adults can meet and greet but babies cannot get hurt.. They really shouldnt be with the flock til they are 2.5 or 3 months old and only after the flock gets to know them through the wire.
I have had roosters for the last year, I have hatched out in the incubator 19 chicks, 7 of which were roosters, I put them in their own run (all the chicks) and when they were almost 3 months old I started letting them free range with the adults, a few weeks later we closed up the chick run and forced them into the main coop...No issues at all..
If there are going to be issues it will be when the young cockerels try to mate with the hens.. Big roo wont put up with that, We try and cull or give away any of our young cockerels the moment we see that they are becoming sexually mature, that is unless we are keeping them