Yup, sounds like lack of comms there.
When running line, I always try and catch ref's eye before flagging. When reffing, I always look to the AR as well if the incident is in their area.
Had one yesterday in a semi final, score 1-0 to red, long ball over the top from black, attacker leaves defenders for dead. 'Keeper comes out but it's hard to read who's favourite for the ball.
Ref has been left behind play as it's the big hoof upfield and he's looking at attacker's back. Ball bounces once and keeper takes a fairly easy catch but attacker runs into her, she drops ball and black toe pokes it in.
I move my flag to left hand to signal and, looking at ref who is looking me, I raise the flag and shake my head. All in less than half a second. Ref trots over to me, "Keeper had the ball in both hands?" "Yep" says I - he blows and signals the free-kick.
Good example of efficient communication, ref suspected a foul so looked to his AR to assist, AR saw the foul and made it clear to ref that goal shouldn't stand. He told me after the game he came over to me just to eat a bit of time and give black a chance to regroup after celebrating a 'goal'.
As a ref, if I have NARs I ALWAYS look to them when a goal is scored, a discreet thumbs up and off to the centre spot for kick off.
