It would appear the pass on your phone is/was valid - it was just not tied into other systems correctly. I've never had this happen, but being an old-school paper type person, I usually also print BPs from website after APP checkin to make sure that works, and almost always get a card BP from an agent at the AP. Takes longer, but I feel better about it. And now that many TSA checkpoints no longer need the BPs (precheck), I feel better having the card in my pocket. Yes, it takes time, but usually not that much. (I usually get all BPs and clear security at smaller stations. My practice woudl probably change if I checked in at a major hub every time!)