I think Atkinson must have missed the kick and therefore coldn't understand why the Assistant flagged. Whatever, it's rare to undermine your associate referees in that manner. Blow for the foul, get clarification , administer any necessary disciplinary action and then proceed with a free kick to the appropriate team.
There was still plenty of time to get the defence sorted after this so we shouldn't really use it as an excuse. However stopping playing and appealing for a ball over the line whilst a feeble cross creeps past you is just unprofessional.