I had the same thing happen to me.
Didn't get any rep for IB, crucible or faction after a win and my medallions didn't get used.
Was just about to make a post of my own but when my last game finished I backed out of the lobby (same one I was in when not getting rewards/rep) and all of a sudden I got all the rep/rewards and medallions gone.
I don't know if your still in the same lobby but back out if pos and see if that helps?
English
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I backed out. I'm sitting in orbit right now deciding wether or not I should play another match.
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I just played another game, my team won and same thing happened again, no rewards, no rep for anything. And backing out didn't fix it this time.