Shaun Maloney struck the winner just after halftime.
"Wigan were the better team," said Ferguson, as his side had an eight-match winning run brought to an end, suffering their first defeat since January in the process.
"They are very under-rated team and we were completely dominated in the first half.
"We were second to every ball and only had one shot at goal. It was one of these off nights you get.
"We have been on a great run and it has put us in a position where we can win the league, so we have to get over the disappointment of tonight."