Flat new hatched

Hey peeps, I can't seem to find a current answer to my question so hopefully you can help. I'm relatively new to raising chickens, only a few months. My question is, is it normal to find a few chicks dead once a bunch is hatched? A couple of months ago, a bunch of 14 hatched & I found 4 that were flattened. Just yesterday, 11 hatched & 3 were flattened. I never have this problem when I use an incubator, so I assume that the mother is the one that flattened them due to space restriction in the nest? Is there anything I can do to lessen this problem?

2nd part of my problem is that my first batch of 6 weeks are getting the Avian Pox. A couple of them already died & a couple of them has so many that their eyes are closed shut. It seems that their constant scatching is making it worst. Is this normal? is there anything I can do?

Thanks ahead for your help!