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Oh, if anyone is interested: since the orbs are not visible, you cannot click them, but not all is lost: they also appear in your "artifacts" tab, with a golden border, and you can click them there. This way, you can complete the level. 

This bug still exists. Level 2 of the heart of gold expension: I've claimed 3 artifacts (booby trap, gold, papa pig), quicksaved, quit the game. After reloading the artifacts (floating orbs on the shrine) are no longer visible but I'm still being "urged" to click on them, the research was complete etc.