I am able to reproduce this easily and have more information. PC 13w07a. I have built rebuilt several chicken farms. My farm is a 2*2 hole several blocks deep. I throw about a whole small chest full of eggs into the whole and end up with large amounts of baby chickens, 50-90(give or take). Now during the 20 min maturation, the baby chickens get pushed into the surrounding blocks. After the 20 min is up and they start growing 2 things may happen. 1. Solid blocks; chickens suffocate and die. 2a. Transparent block space behind, x amount of chickens get pushed through the block entirely. 2b. Transparent block, solid behind; chickens stay in the trans block until they wander out after enough room has been made.
Edit: the transparent block i used is glowstone. Dont know if it makes a difference though.
Pre 1.5. I can confirm that the same exact thing is happening as my previous post.