It's really only happened with the weapons gained from Challenge of Elders.
For instance, when a weapon's fully upgraded, it's thumbnail is highlighted in yellow, but when the Queen's Exotics (QBB, Dreg's Promise, Lord of Wolves) are fully upgraded, it still shows the green bar below the weapon inside the thumbnail. This is just a bug, I presume.
I know it's small but man is it bothersome.
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Any weapon with chroma slot not activated will show as not upgraded once you insert chroma in it it'll show as fully upgraded. Except PoE Exotic Y2 they are bugged as far as I know.
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Other threads claim that they will not show as fully upgraded until they are at 335.