Level 100+ weapons not increasing skill in the menu is working as intended, not a bug, as they don't want those weapons to enable access to weaponskills that your job normally doesn't have the skill level for at level 99. When they released iLevel equipment, they stated that in the patch notes.

The bonus skill levels in the equipment stats are the need only one stat to show you how it affects damage and accuracy. More skill = more damage and more accuracy.