From my understanding, you have to get to a certain level before you are allowed to buy any bonus level.. Right now, enjoy the "lingot-free" levels.. There are a lot of things you can learn/review until you're able to buy them.
I have completed the tree, but still have a space open for a bonus skill. When I go to the lingot store, there is no other bonus skill for me to purchase. I have plenty of lingots. Any reason why?