The reason this happens is because you don't really get the rune as your actual coin amount is not what your display says. Sometimes rewards given out to your HUD can be paid multiple times giving you wrong totals then the actual amount you account has.
For this graphical reason I would suggest you always refresh the game after cerb and baal, 2 of the main culprits for giving out wrong information to your HUD. And possibly even refresh before you go to use the rune temple for anything significant. Refreshing will give you the correct amounts of coins/credits/gems your account actually owns and you will never see this issue again.
At the end of the day you can't lose what you don't own, BUT it would be nice if the game didn't give you wrong information which means constant refreshes are needed.

