I can't be sure this works for everyone but it fixed it for me!!! Highlight whatever item you want to remove in the sanctuary box, whether it's a named animal you can't stack or an incomplete stack of berries or mushrooms or whatever, and instead of "grab" or "move to inventory" select "drop." Then it will ask if you are sure you want to drop this item, say yes. Then it will appear in your inventory. Now you can stack unnamed animals if that was your issue or else stack the FULL amount of berries/mushrooms/fish/etc. all at once! I really hope this works for everyone like it did for me.