The 39-year-old Latics manager lambasted the referee's display during a recent game between the two sides at Old Trafford and has been charged with bringing the game into disrepute
The charge relates to an alleged breach of FA Rule E3 concerning media comments which imply that the match officials are motivated by bias or have brought the game into disrepute.
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"We want to come to places like this and get results like we did at other big venues last season, but you know it's going to be a tough ask when decisions start to go against you as early as the fourth minute," Martinez told the club's official website.
"Welbeck should also have received a straight red card for his challenge on Franco [Di Santo] at the end of the game.
"You need mentally strong referees to make these decisions regardless of their surroundings and the teams playing, but unfortunately I thought the game was too big for the referee."
The Latics boss now has until 4pm on Thursday 27 September to respond to the charges made against him.