This will show you how animals are added to the zoo count when you purchase or acquire them again. For this example we will use the Green Dragon.
There are currently 2 green dragons on this island. We will show you what happens when you purchase another one.
The shop currently shows 2 green dragons before the purchase. The next image shows the purchasing action of another green dragon.
Upon the purchase, the shop shows 3 green dragons. Since the green dragon was already owned prior to this purchase, it added to the count and now reads 3 as shown on the island.
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.