Body Armor, Helmets, Relics, Uniques and Sets can all have affixes which grant additional levels to certain skills. These affixes can exceed the normal 20 level limit of skills.
Any skill levels currently granted by items will be shown in blue above a skill's XP bar inside its skill tree.
Unequipping an item which grants levels to your skills will remove points from them, unless you have a number of unspent points greater than or equal to the levels lost.
Nodes which have lost points in this way will be highlighted in red when you next view that skill's tree.