It can't be the player's responsibility if by simple accidentally clicking on a mound you instantly unlearn two skills - that's crazy. A simple "Confirm / Cancel" prompt should be enough to avoid that.
I'm not against a confirm/cancel thing, or making the extra skills unusable.
I meant that the player is responsible for learning skills beyond their base capability. Those extra skills didn't just appear in your list by accident, That was something you have to do deliberately. The Ability-Skills tooltips show you how many skills you can learn, and if you have any points boosting the base.