I built two simple cells with a 4x4 base and 3-high walls of glass or stone. Then I used eggs to spawn baby chickens. The babies lived happily in either enclosure but soon after becoming adults the chickens enclosed in stone began suffocating. Eventually all died. I changed the floor to hoppers to show the results. With 16 chicks to begin with, glass results in lots of eggs, and stone results in a few eggs and 16 chicken (meat) and a similar number of feathers.
Four pictures illustrate the setup and the bug.
The same problem occurs if any of the surrounding blocks are solid. In my pictures three of four walls were stone in the deadly case, but chickens will die if only one of the wall-blocks is solid.