I had this problem for 2 days now, anyways I've been doin my bounties and stuff to get the vanguard XP. Suddenly I stopped getting anymore XP for vanguard...need help I'm only lvl 1 vanguard reputation, oh yes there's this different icon that shows up instead of the vanguard.
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It definitely sounds like you equipped a faction class item. Just swap out your class item to one that isn't for dead orbit, new monarchy, or future war cult and you'll get your rep gains for vanguard back.
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Are you sure it's not crucible or iron banner?
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Did you put on a different cloth on your setup? Some cloths make you earn points for different factions...