There is an ongoing issue with the quests for books. It seems all books (or at least some of them) are considered equal, which means if for example you have the "Roots" book it counts as the "Natural Aura" book. Also I think that happened with the Hearthwell book because it completed although I didn't create it, but I don't remember which other book I had in the inventory back then.
When you have JEI show you the recipe for a specific book it shows you the recipes for all similar books, including the "I" tab for the Book of the Well, probably for the same reason.
Books in the same JEI recipe:
There is an ongoing issue with the quests for books. It seems all books (or at least some of them) are considered equal, which means if for example you have the "Roots" book it counts as the "Natural Aura" book. Also I think that happened with the Hearthwell book because it completed although I didn't create it, but I don't remember which other book I had in the inventory back then. When you have JEI show you the recipe for a specific book it shows you the recipes for all similar books, including the "I" tab for the Book of the Well, probably for the same reason. Books in the same JEI recipe: