First of all, thanks for this great game. It is fun and easy to play.
Question: For example, when all players discovered the same clown fish. The clown fish will be removed from the game. What happens with the player tokens on it? Will it go back to the owner so he/she can discover more than 12 animals?
From this, I guess we can presume that you cannot discover more animals while you are out of tokens? You need to wait for animals to be fully-discovered or swim off the board.
You can make that a house rule if you wish, but officially the amount of discs should be unlimited and be replaced with whatever object, or you can remove a disc from another animal you will never visit again anyway.