Here’s the hard truth of raising poultry:
They have lots of offspring in a brood… because many of them are destined to be weak and die in order to feed other animals. Think baby sea turtles on a beach. Most of them exist to be eaten by something else. Only a small number will make it to adulthood to reproduce: the most vigorous, toughest, strongest ones. That’s the way of things with animals with high reproductive rates.
In the wild, only 30% or less of wild red junglefowl make it to adulthood, then of those that do, only a small percentage of otherwise successful adults ever consistently make their own offspring that survive to adulthood. The most elite of the elite survivors parent the next generation.
Enter our artificial way of keeping fowl. We often coddle many weakling birds out of pity. When those birds may have always been meant to be culls to serve a purpose other than their own well-being.
So the long and short of it is, you’re not necessarily doing anything wrong when some prove more weak than others and cull themselves out of the gene pool. Sickness is a major factor in natural selection among birds, far more than predation. Many millions of birds in the wild can die in a geographic location due to sicknesses, wild birds infinitely tougher than our artificially bred domestic fowl.
Sometimes you got to let sickness do its thing. Cull the weak. Best way to get through it is to have a large flock. Inevitably some will be tougher than others and thrive through the sickness. Those are the ones you want to let reproduce.