I recently played a game as 
where I got mastery 5 and an S in the same game, but didn't get a mastery 6 token. I am not certain if this is a bug or intended, but I do feel like I was cheated and I'm sure when this happens to other people, they feel the same way.
It is intended.
I've gotten S several times before hitting Mastery Level 5 on a champion. I feel cheated, sure, but I know those are the rules. ;)
Your S ranking got you to Mastery Level 5. It can't also get you a Mastery Level 6 token.
This is not a bug. You got an S from a game in which you played a champion that you only had at mastery level 4. It was not eligible to earn tokens. You have to complete a game and get an S- or better on a champion you HAVE at mastery level 5.
Feels cheated, sure. But it's not a bug.
