I used a rune of cleasing to remove all mods on an amulet. After crafting t5 dodge rating and t3 dex somehow the item was not recognized as being on the craft window crafting wise. It can not be modified but the graphic remains there and the item is not found anywhere else. When I put another item over it, it shows the mods of the previous amulet. The two graphics of the item overlap each other. Only when I specifically mouse over the new item (not the amulet) does it show the mods for the new item. The mods in the crafting window are still the amulet. It is not fractured.
What were you doing at the time?
How consistently does this happen?