As you go up the Mastery tree, you will buy squares and shade it yellow. Eventually, you'll come up to an ability. Just because you shade over the ability doesn't mean you learn it. You have to click that ability to actually learn it. Here is an example.
Look at this build: http://www.wardb.com/career.aspx?id=3#0:0:15:0:0:0:25
Now look at this build: http://www.wardb.com/career.aspx?id=3#0 ... 928:0:0:25
In the 2nd one, do you notice that Master Rune of Speed, Earth's Shielding, and Valaya's Shield now are outlined in yellow? That means I purchased them (which costs an additional point). In the first link, I spent 15 Mastery points. In the second link, I spent 18 points. You are not clicking the ability to buy it, obviously.
ps: I'd laugh at you, but I made the same mistake. I didn't petition, though.
