If the older chickens were still chasing the younger chickens around and the younger ones were going to their own run at night, then I would say that they hadn't accepted them into the flock, yet. I think when it was time to go to roost, the older chickens could have killed the younger chickens that tried to invade their roosting space. If it was a predator, why kill just the younger ones and not the older ones, if they were all in the same space? I would look at the run security, just to make sure, but it seems like an awfully big coincidence.
It's so much easier to just get all the chickens you want all at once, rather than adding them in later. Sometimes it works and sometimes it doesn't. I'm not really sure what you should do, at this point. If you cull them, you'll still need to get more chickens, right? Can you get any that are close to the age of the 3 week olds? Even day olds would only be a few weeks behind. When they were closer in size, you could combine those flocks. Young pullets hopefully wouldn't be as aggressive as more mature hens.