But replays showed there had been no contact on the Birmingham winger but James McFadden scored the resulting penalty to settle the issue.
To make matters worse for the Latics, James McCarthy suffered an ankle injury in a reckless challenge from Liam Ridgewell and now looks set to have to pull out of the Republic of Ireland's friendly international with Brazil in midweek.
Martinez said: "For the penalty, I don't think there was any contact and, if there was any contact, it was certainly not enough for it to be a penalty.
"It is quite clear. The referee was only five yards away but at the moment we are not getting the luck with decisions.
"Our player is trying to clear the ball and, their player, I would say should have been given a yellow card."
Ridgewell escaped punishment for the touchline tackle on McCarthy but Martinez claimed: "It was an horrendous tackle and McCarthy's ankle is quite damaged.
"I don't think he will be able to play against Brazil which is a shame because it is his first senior call up.
"He will meet up with the squad but, the way he is now, he looks unlikely to be able to participate."
Martinez felt his side deserved something from the game but believes they still have to improve in the final 11 games to stave off relegation.
He said: "The first half was a poor game in terms of quality and our performance was not good enough.
"In the second half, we were more like ourselves in terms of determination and posing a threat. We deserved something from the game.
"But everybody needs to improve and put in that extra five per cent over the remainder of the season."
In contrast, Birmingham have now reached the 40 point mark for the season and assured themselves of top flight football for a second successive campaign.
Blues manager Alex McLeish said: "If you had said at the start of the season that we would get 40 points by March, I would have said you are having a laugh because the squad needed time to gel and develop and we had lads coming in from the Championship.
"To get to 40 points before March is an outstanding feat from a squad that cost £10m in the summer to assemble.
"That is amazing and it is even more amazing that we are in eighth position but we now want to kick on and the characters in the dressing room will ensure we don't ease up."
McLeish had no sympathy over Wigan's claims about the penalty being harsh.
He said: "Melchiot put his foot in and when you don't get the ball you are always risking it as a defender.
"It was a bit fraught and anxious in the second half and Wigan threw caution to the wind but once again Joe Hart made a couple of fine saves to earn us the extra two points."
McFadden converted his spot-kick in first-half stoppage time for his third goal of the campaign.
It also enabled City to complete a double after a 3-2 away win over the Latics earlier in the season.