Passive animals have a chance to glitch through corner fences. This mainly affects chickens because they congregate in the corners of pens. This "feature" lets animals escape pens that have no holes or any way for them to get out. The chicken in the picture had been in the fence until I had seeds in my hand and it just walked out of the corner of the pen. This may also be the cause of my chickens disappearing. It happens more often when loading and unloading chunks. (Probably because chicken is "in" the block so it can walk out easily when re-loaded.)