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.

Exactly- you need to reach far enough down the tree, and you'll be able to unlock them.

Roughly how far do you have to get?

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?