Fences appear to be 'leaking' animals. Chickens, sheep, cows, etc are found outside of their fences seemingly at random. Have not witnessed such a leak, but leave the chunk regularly and return with a few escaped animals – but not all and not the majority. Thought it might be a reproductive crowding issue, but have now witnessed it in animals I haven't been breeding, either. (Have not seen this issue with any prior versions of Minecraft.)
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Possible you have more animals than what can stay in the fenced in area. Try making the fenced in area larger or removing animals.
Dupe of MC-2025
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