I had the same issue yesterday. What worked for me is to go back in game and switch to party member (in upper left corner) you want to edit skills for. After that, it worked as it should, the skills stick when applying. Same goes for other followers (I had Cass, Varrick and Solus, but I believe it'll work on any follower)
[Edited by marsaxlokk, 11/28/2014 2:33:32 PM]
Had a strange issue like that myself, I was able to unlock all the abilities, but when I travel back to Haven I got a message "Abilities points refunded" and all the abilities were reset.
I just unlocked them in Haven and they seemed to have stuck now.
Another issue was the Super Gold Sale, after you turn it off and go to a vendor again the game will crash.
Again no biggy, I just gave myself a good amount of gold, saved and started the game again.