After you put the crystal in, there's a little button on the bottom right that you need to click in order for the change to occur, did you click it? Also if you were placing the new crystal on the old crystal you will also get a pop-up asking if you really want to do this because it will destroy the old crystal (this pop-up appears after click the apply button), did you say yes I really, really want to do this?
Check if the new crystal is still in your inventory.