I just realized that I found a bug with the Skill learning. I am on a Wizard so i don't know if it is affecting other classes. When upgrading skills sometimes it takes the skill points without learning the skill. For example sometime upgrading Fireball explosion from II to III the points are taken but the skill moves up the list one spot and still says III. This bug is causing you to have some skills that you have to spend the point twice and wasting them. I have checked the "Main" tab and the skill will show FB Explosion II before upgrading the second time. 

In the attached pics you can see its not always the same upgrade level and it also happens to others skills like Magic Missile. In Pic 1 I start at full reset 466/466, in the second pic 5 points are taken for level I, In pic 3 10 points are taken for level II and the Skill stayed as Level II and moved up one slot, in pic 4 another 11 points are taken for level II and the upgrade worked as you can see the next option is Level III. I can't even get through a full build without this happening with multiple skills wasting a fair chunk of skill points.

*Sorry for photo quality, was taken via phone 

As a temporary fix it seems that if you move to another skill the go back to upgrade it works.

Nice to know I'm having the same issue will check if this works ?