In the Characters menu, there's an orange "UPGRADE" notice next to my Gems display. I checked at a rest site and saw I didn't have enough materials to upgrade my gems, so what is this notice for?
When the "UPGRADE" message appears as such, this means you have recently1 upgraded an existing gem, or crafted a new one. By navigating to the gem selection screen in the character menu, a gem will have an orange dot on the top-right of it indicating it has been upgraded/created. If you hover over all the gems with this dot, the "UPGRADE" message will go away.
1 Recently is relative, since this will stay as long as you have unchecked upgrades.