Shaun Maloney's strike early in the second half was enough to secure the Latics their first Premier League win over the Red Devils.
However, Ferguson believed that his team should have had a penalty when the ball looked to have struck the arm of Maynor Figueroa with 15 minutes to play.
"Figueroa did handle it and the thing is that if he'd been close to the ball then you can say that you won't get those, but he was at least 15 yards away. It's a clear penalty," the Scot told BBC Sport.
"That's disappointing but sometimes you get the breaks and sometimes you don't - it evens itself out over the season.
"We had a break on Sunday. You say the big clubs get the decisions, but we didn't get anything. Phil Dowd had a disappointing night, he never got to grips with it."
Despite the defeat, Ferguson was quick to give credit to Wigan's performance.
"We only had one shot on target and we were second to every ball," he added. "You have to recognise that Wigan are in a false position, they play some of the best football in the league you have to credit them for that."