Despite the factual nature of the comments, Martinez is still likely to be punished by the FA for upsetting the apple cart, or the revenue earners of Manchester United.
The Latics boss said: "I have come to United three times before today 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.
"There were tackles flying around that if they had been the other way round there would have been a couple of red cards."
Of the charge, the FA stated: "The charge is in relation to 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."
Martinez has until 4pm on Thursday to respond to the charge.