The warning appears to happen periodically as I move around the world (nothing changing dimensions required), However sometimes as our spawn town loads and unloads many such messages appear, and as mentioned by Žilvinas the passive mobs in the area appear to despawn.
On 15w32a yesterday both our cows and chickens in addition to a randomly pig trapped near us despawned. today 15w32b the ckikens did after many messages such as:
[17:57:18] [Server thread/WARN]: Tried to add entity Chicken with duplicate UUID f57f94b0-d2ef-4b8e-86c1-edadbf33c3f3
Just fished 7 of these enchanted books w/o enchants in version 15w32c