So, are you saying that your mentor "isn't working"? If the skills are actually being removed (meaning the mentor "is working"), then you should first acquire all the skills needed for the Special Ability, and then generate skills in those skills in the remaining two slots. Do you have a "skill wheel"?

Added 1 minute ago
By the way, this may also depend on the hero's class. For some, the path to the Special Ability is more suitable for their class, and for others, less so.

Added 1 minute ago
Oh yes, have you developed all the skills in the class skill (the one that is "counterattack," "master of artifacts," "opening of portals," etc.)? If not, then of course the skills you need won't appear.