So I was doing the Weekly Heroic Strike with my friends when I was disconnected at the last second before Phogoth was destroyed, when I am able to rejoin my friends are already out and now it says that I have completed the Heroic but I have received none of the rewards
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It is a bad idea to join a mission in progress of those in it are about to complete it. Exactly what you described can happen. When someone on my team d/c's, the rest of us hunker down and avoid killing the boss, until our team is back in the game again.