Hello,

Level 13 witcher - not getting extra ability points from quests (Bloody Baron- all finished), I've missed like 7 of them, and then, after levelng up I'm getting message, that there are two points to spend. On character screen - there is only one.

Edit:

21 ability points, with 6 places of power visited.

You're supposed to gain ability points every time you level up and / or you draw power from a place of power. That is 1 ability point for each level and / or place of power. At level 13 you should have gotten 13 ability points by leveling up alone, plus another 6 from the places of power you've visited, so a total of 19 ability points. You cannot get ability points by completing quests alone (although completing quests grants you exp, which leads to leveling up, which in turn gives ability points).
You either have spent your ability points on mutations (the brown coloured category of the character abiity tree) or there is some bug issue. I haven't encountered any similar problem.