If you own an animal previously and then acquired it again it will add to your existing count.
By acquiring we mean Shop purchase, gifting, or Watch and Earn.
This means that the number of where the animal is updated. If this was on an island the number should change. You can check if you owned it already through the search bar in the Shop or Storage.
Animals you owned already will NOT go to your storage if you acquire them again. They will just update the existing number you had already.
The design of the game is that any upgraded, gifted, or purchased animal that you already own will add to your zoo count and not show up in your storage. Hope this clears up any confusion or questions about missing animals.