Equipping an item that gives bonus skill points, allocating the skill point then unequipping the item has very weird result: as expected, the number of skill points reverts back to the original, but the exact skill point removed is not the one lastly allocated!
It happened to me with Elemental nova, where after using the skill point on +crit damage, it then substracted a point on +elemental penetration. This doesn’t seem to be random, as equipping the item again and doing the same process twice got me at -2 elemental penetration for +2 crit damage.