The Latics manager was frustrated to see Manchester United awarded a first-minute penalty last week when replays showed minimal contact between Danny Welbeck and goalkeeper Ali Al-Habsi.
Martinez feels calls often go against the lesser sides in the Premier League and finds hard to understand why.
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"It's understandable, but goals happen in the game and they will happen, it is part of our game. It is difficult in certain aspects, certain games that you never get wrong calls going your way.
"From that point of view, the disappointment you get when you can see in two or three games on the trot, playing against certain teams, and you don't get that measurement that you feel you should be in a normal judgement of two teams.
Despite his frustrations, Martinez feels his squad must concentrate on their own game and keep improving after making a solid start to the campaign - taking four points from their opening four games.
He added: "It is not a good aspect to keep talking about referees this season because that's not going to give us points.
"What we need to do is focus on ourselves, when you assess the game you need to move on from this and just try to see how we can improve, how we can be better and how we move on to a better level of performance and that's what we will carry on doing."