To take a closer look on it I need more details. After adding EXP (did you add more than you need for next level up? That can cause bugs), which points were vanished? Attribute? Skill? Talent?
For the health option make sure you don't use it outside of battle.
And yes there are several caps. Therer is are skill caps, level caps and I also think attribute caps.
Yep, that did it. Tried adding just enough XP so that the next quest or kill would get me that level up this time instead of leveling up using only the XP option and it works without removing the points, tried that three times back to back and neither points nor health start glitching out, thanks for the heads-up!