Hughes was sent to the stands during the first half of Stoke’s 4-0 defeat at home to Tottenham on Saturday after showing his displeasure at referee Anthony Taylor for booking winger Marko Arnautovic for diving.
The Potters have expressed concerns about inconsistencies shown by match officials towards managers leaving the technical area and have questioned why fourth official Jon Moss prevented Hughes communicating via mobile phone from the stands after his dismissal.
But they will not be challenging the FA rap and their boss could now be facing a touchline ban.
A statement from the club read: “Stoke City can confirm that although Mark Hughes disagrees with the Football Association’s charge of improper conduct levelled against him following the game between Stoke City and Tottenham Hotspur last Saturday he will not contest it.
“Notwithstanding this, Stoke City does however have concerns in relation to a number of elements surrounding both the decision to dismiss Mark from the technical area and the events that followed that led to the subsequent charge being brought.
“Based on other Premier League matches played on that weekend, the Club is concerned in particular that there has been a potentially inconsistent approach in the enforcement by match officials in instances of managers leaving their technical areas, together with an incorrect application of the Professional Game Match Officials Limited’s own guidance note on the use of electronic equipment in the technical area in respect of a manager communicating with technical area staff from the directors’ seating area after Mark was dismissed from the technical area.
“The Club will be raising these issues with the Football Association and the Professional Game Match Officials Limited separately.”