This is really strange. Placing red gems on beacons manually during play seems to have the same problem...you can't pick them back up. I thought maybe the gem was the problem, but you can pick them back up from alcoves and altars just fine. So it's specifically the gem and beacon together that cause the issue.
I tried adding a connector to the beacon's clickable component that would remove whatever item is in beacon and place it on the mouse pointer and that worked okay (it removed the gem correctly), but I'm bad enough with sockets that I couldn't figure out how to set the item count back to 0, so the beacon wouldn't accept any more items after that.
So...really I don't have a solution to your problem. But it's VERY interesting!

I'm curious if it's a bug or intended.