Town boss Joe Royle said after the match: "I can't argue that Wigan deserved to win especially after their first-half performance but I have to say it was never a penalty.
"The incident occurred outside the box and the players actually ran into each other. The referee did well but he had one big decision to make and he got it wrong.
"At the moment we don't have a goal in us. We have never been good at keeping clean sheets but the goals have dried up at the other end."
Wigan boss Paul Jewell said: "I know it's a cliche but nothing has been decided yet and there are still 33 points to play for.
"The result was important because of who our opponents were but it's also a further three points towards where we want to go.
"In view of the problems all week when we had only nine players fit to train I can't speak highly enough of their commitment.
"We did not know what the team was until 1pm today when all the players reported in and I have given them all a day off on Monday to try and rid the club of the bug."