Since the last update, some gems are now invisible.
The AI matched both red and blue gems to invisible gems.
official ticket sent in with screenshots
(edited to add screenshot)
This has been happening for a while now, since about August I believe. It usually happens when a clue gets destroyed due to a landfall and then the clue space becomes blank.
OK, this is the first time I’ve seen it and I searched before reporting it.
Don’t worry, that’s not what i meant, I was just backing you up 
Our team has seen that pop up a couple times during our games this past week. We’ve already notified the development team, so rest assured that they’re aware of the issue.
This has happened to me dozens of times in all of the previous 3 or 4 releases. And I can say that I don’t think any of the times had to do with Clues being popped.
Happened to me too. But less often.