Yesterday and today I have not been getting rep from doing any patrol missions. And I did quite a few without realizing it.
Quick rundown of my steps after bug:
I had a exotic weapons mission that auto-completed. (Awesome, by the way ;) )
I got my faction mission from Future War Cult.
I had 8 bounties completed and ready to turn in. So I went from 32 to 34 immediately.
Ran around with looking at new content / dissembling my emblems and shaders, etc. for room.
Did all the PvE missions for the day.
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Yeah, I noticed this too. Hopefully bungie fixes this because if they don't the reasons to go on patrols go down drastically.