Not specifically a "bug" but the introduction of the Chicken Jockey seems to have created a new problem:
The Jockeys spawn in and eventually despawn but the Chickens remain - the chickens then proceed to lay eggs - the eggs are picked up by newly spawned zombies - and eventually there are hundreds if not thousands of egg-holding zombies that cannot despawn in a cave somewhere.
I was just about to add this problem but I know exactly what you mean. This has happened twice in my world and it is problem that is just way too annoying.