The Latics boss was critical of Michael Oliver after the young official found awarded several controversial decisions against the visitors at Old Trafford
The hosts were awarded a dubious penalty in the fourth minute when Wigan keeper Ali Al-Habsi challenged United striker Danny Welbeck, but appeared not to make any contact. But the Oman stopper denied Javier Hernandez from the spot seconds later to see justice prevail.
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Goals from Paul Scholes, Chicharito, Alexander Buttner and Nick Powell in the second half were enough to seal victory for Sir Alex Ferguson's side, but Martinez feels the lack of decisions in favour of his side heavily impacted their chances of gaining some vital points.
"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.
Martinez also believes that Oliver made the wrong decision to only book Welbeck for a crunching challenge on Franco Di Santo, and claimed the pressure of the game was too much for the 27-year-old referee.
He added: "Welbeck should also have received a straight red card for his challenge on Franco 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."
Wigan face Fulham at the DW Stadium on Saturday with the hope of returning to winning ways after a steady start to the season which sees them lie in 14th position.