Are you talking about the console command that allows you to respec? How exactly can I reproduce this situation?
I mean if you use the command "AddTalent fast_runner" you will get the fast runner talent, but on the character sheet it will be listed as an ability.
Additionally when levelling up you will still be able to choose Fast runner under utility and spend a point on it, which adds Fast runner under talents giving you two Fast Runner instances(both work as intended).
So really its more of a graphical thing and being careful with doubling on talents.
As I said its a minor thing that really isnt necessary to fix per se, its just an inquiry if its intended that talents get put under abilities and dont get removed from selectable level up talents.
(Used this command thinking I could move faster with fast runner, turns out its combat only, though it can have comical effect if stacked having enemies trying to catch up while you leave them in the dust)