I'm not sure if it's a bug or what, but I have had a few characters run into an odd phenomenon where I would add points to their skills - but the total skill value (after synergy bonuses / penalties) wouldn't change. I've made so many different characters, though, that I honestly can't remember which ones I had this problem with.
I want to say that it was something I only tended to encounter when heavily investing in skills with multiple synergy bonuses.