The Gunners thought they should have had a penalty after six minutes when John Egan pulled Sokratis back by his shirt as the hosts defended a corner, but referee Mike Dean was unmoved, and VAR was not consulted.
And five minutes after Lys Mousset's goal which turned out to be the winner, Bukayo Saka was booked for simulation as he went down under a challenge - again from Egan - inside the penalty area.
Speaking to Sky Sports News after the match, Emery wondered why the incident involving Sokratis was not sent to VAR.