I had something similar happen to me after I respect a passive tree. Instead of getting 2 points from the Merciful Agony I only got 1. After looking around I found that the point from a passive tree I had removed was back. So no issue was found just odd that it did that. 

Huh... I had my xp indicator go to -90 after gaining a level once, and it locked me from gaining xp and didnt give me a higher level, the level up rewards screen or my points. I quit the game and logged in as my other character, played a bit, then switched back and i had my rewards screen, points, higher number, lost xp and other rewards all dropped on me at once. I dont feel like thats likely to work for you, but dont worry, im sure theyll give your points when they see ur post. They should really debug their server code a bit more. When someone makes a game wholly dependant on online servers they really ought to work better.