Are you breeding them, or throwing eggs in through the top, or have some automatic egg throwing mechanism? (I don't see the latter but it looks modded so I'm not sure what could be there). If it's throwing eggs related, I think from time to time I've had baby chickens spawned that way end up inside the side if a block where they immediately suffocate. I'm not sure glass has that suffocating effect because it's a transparent block, so maybe some of the chicks spawn glitchily partly inside the glass and some of them manage to get out the other side of it somehow?