My initial question was geared more toward if he was being overprotective since there was a predator attack recently that occurred in/around the run, but now I am panicked that I've messed up.
Yeah, like Tonyroo said, it's not a kindness or good act from him.
A cockerel that age is full of breeding hormones he doesn't know how to handle. Think 18 year old male.
The pullets are pre-pubescent, still just chicks. They don't have defenses against his desire to mate.
He's not herding them into the coop, he's trying to corner them so he can get on top of them, and they are running away to the only place they've felt safe before.
Of course, he can always just come in and do what he wants, because he's so much bigger and they're still timid chicks that don't know how to protect themselves (mature hens face off with a rooster so he can't get behind her, that is way too intimidating for chicks to do). So, the entire time they are hiding in the coop, they are worried he's going to come in.
The hormones of a pullet don't kick in until she's laying eggs, that's the only time she's a willing partner. Any mating before that is rape.
I realize criticism is hard to take, but for your future success with chickens, you should know that the area you described for the pullets under the nest boxes doesn't sound big enough for humane housing.
Feel free to post a picture if you want to talk some more about how to use the space.
The cockerel as a single bird should be the one locked up so the many can have more freedom.
You may also be able to integrate your younger chicks with the 2-month-old chicks as soon as the younger set have feathered up.
And if you post up a new thread of your own, a lot more people will see it and give you their opinions.