If you leave animals penned in one area there will be a build up of manure. That manure can be both unhealthy for the animals, and the build up of nutrients can be unhealthy for the
land if concentrated.
Industrial farmers rely on slurry pits and then using machinery to spread the manure on the fields.
In a
permaculture system you would aim to avoid that problem in the first place, by avoiding concentrating manure in one place.
Eg
cattle might be rotationally grazed with only a day or so on each piece of land. The manure gets evenly spread, and the cattle don’t end up standing in it.
Chickens might be “tractored” around the land, moved every day. They get fresh forage each day, and the manure is spread where it falls onto the grass.