I created a new document in Photo (1.9 RC1).
I added a simple rectangle, gave it a fill color, and used Duplicate Linked.
I then did a copy/paste, which actually pasted another linked rectangle - ok...
I then unlinked that rectangle by clicking the topmost link icon in the Links panel, but the link indicator still shows in the Layers panel, even though in theory that rectangle should no longer be linked at all - correct?
I then did a copy/paste on that rectangle, and the new one also shows as linked in the Layers panel, even though it is not actually linked to anything (color changes independently).
It seems there is some kind of issue with the link indicator in the Layers panel.