Martinez has been charged with "an alleged breach of FA Rule E3 concerning media comments which implied that the match referee and/or match officials in general are motivated by bias and/or brought the game into disrepute" for his comments made after the match at Old Trafford on Saturday September 15.
The Spanish coach has until 15:00 on Thursday to respond to the charge.
Javier Hernandez could have opened the scoring after just five minutes via a penalty awarded by referee Michael Oliver for a foul on striker Danny Welbeck by Ali Al Habsi, but the Wigan goalkeeper saved the Mexican's effort from 12 yards.
After the match Martinez was critical of the decision to award the spot-kick after it appeared that no contact was made between Al Habsi and Welbeck in the incident.
"I was (irritated)," he said. "You could see it. You know what (Welbeck) is trying to do."
Wigan have never picked up so much as a point in their eight league visits to Old Trafford, and Martinez expressed his frustration at being the away side at the Premier League's biggest ground.
"I have come to United three times before today," he said, "and for whatever reason we don't seem to be measured in the same manner as the team at home.
"Today the penalty is as bad a decision as you are going to see in the Premier League.
"In many ways, you feel as though you are fighting against a mountain."
Referring to another incident involving Welbeck, in which the England striker lunged in on Wigan forward Franco Di Santo, Martinez added: "There were tackles flying around that if they had been the other way round there would have been a couple of red cards."
United eventually ran out comfortable winners courtesy of second-half goals from Paul Scholes, Hernandez, Alexander Buttner and Nick Powell.