It seems the game does not properly keep track of the amount of +skill level gained from items.
In this example, I’m using a Judicator, giving me a +2 to javelin.
However, the skill menu only shows my points as 20 total (despite me having allocated 22, count them)
If I re-equip the item, the tooltip temporarily moves back to level 22, with 2 points available.
However, the moment I allocate any skill point (in javelin or another skill) the tooltip jumps back to 20. I am still able to allocate points 21 and 22.