There is definitely a bug there somewhere. You have more food than your barn can hold and there is still someone out stocking more feed? That alone is glitched.
It may be because they haven’t finished milking the cows. The cows can’t go out and so they are unhappy and become unhealthy. I had the same problem with tier 1 barns. If you disable milking, the cows will be able to go out and they should get better.