It shows you the mastery 6 token as if you had it but it doesn't actually adds it to your loot.
One case should be chosen, either the token is shown and given or it's not shown at all... it's quite the cock block really.
You cannot earn a mastery token for the same game you reach mastery level 5 with a champion, only for games afterwards. The notification that shows up (or at least should show up) is stating that you are now eligible to earn mastery 6 tokens with that champion, not that you have actually earned one. The two do look very similar, though.
I reported this bug around 6.8 or so. Still hasn't been fixed.
