United were the beneficiaries of a generous decision in the first half when Wigan had a goal chalked off, correctly in the eyes of Ferguson.
The champions then fell behind to Shaun Maloney's 50th-minute winner, which came from a corner that should not have been awarded according to Ferguson. United then saw strong penalty shouts for handball against Maynor Figueroa waved away, and the Red Devils' boss was not happy.
"We had one a couple of weeks ago against Fulham when they claimed for a penalty when the ball was drilled from close range at Patrice Evra. You're never going to get those," Ferguson told Sky Sports.
"But when the offender is 15 yards away it's a different matter altogether. The linesman's clearly in view of it so that was disappointing. It was a penalty kick."
Turning focus to Wigan's goal, Ferguson commented: "It was a bad kick. Clearly a bad kick. Phil Dowd had a disappointing game tonight, he never got to grips with it, but that doesn't take away from the performance of Wigan tonight - they deserved it.
"We were completely dominated by Wigan; by playing three centre-backs they had a lot of time to build from the back. We went against them a bit more in the second half, but in the first half we were dominated.
"It was an off-night that you sometimes get in football."
