My team was flagged for offensive holding during an interception return, which resulted in me still getting the ball (good), but the interception was not recorded for my player: https://mfn16.myfootballnow.com/gamecenter/view/1996#350565
I had this happen to me twice on offense now as well. Both times their was a holding call while a receiver was running with the ball, so the holding happened in the middle of the play. Both times neither the receiver nor the QB had stats recorded for the play.
I just let stuff like this slide now, at the end of the day its just NOT that important. I see stuff like this all the time, the most common is unrecorded sacks.