Ideas
Im having the same issue!
Ive tried selling the shed then buying a new shed. Ive tried purchasing another animal and it just goes to my household inventory. Ive tried using cheat codes to size the shed down and back up. Ive tried assigning the livestock to the shed and it doesnt actually put the animal in the shed and then the animals are all grayed out. It wont let me place them from my household inventory either it keeps telling me they can only be placed on certain objects.
The only thing that kind of worked was moving to another house and then moving right back, then sell the shed and buy a new one, purchased a new cow, it actually put it in the shed. However I still have 3 cows and a llama stuck in my household inventory that I cant do anything with. This bug is extremely frustrating and there doesnt seem to be a fix.
I dont want to delete my family and start a new one, I built the home from scratch and worked hard on building up the family's wealth.