Generally, you should include: What went wrong?
This issue can arise when you equip two items that give +N to skill levels where N can have more than 1 value.
If I equip either Hakar’s Phoenix A or B I get +2 skill levels as expected. However when I equip the combination of A+B or B+A it only gives +3 levels instead of the expected +4.
I also had this kind of a bug with different +X skill level items but for me it was only a visual bug. I changed +1 skill level to +2 skill level (manually took one away and placed another, didn’t use quick swap) and my skill level dropped down instead of levelling up (18 + 1 to just 18 when 18 + 2 was expected) but I still could spend my extra skill point even tho the game was showing I have 0 available. Have you tried this? Oh, and after I pass any loading screen (just teleport somewhere) it shows everything as expected.