The Latics went into the game on the back of victories over Manchester United and Arsenal and took the lead courtesy of an Emmerson Boyce strike.
"It was one game too many for us. I thought we looked a little bit tired, which you would expect if you compare our preparation- with three tough games in eight days - to Fulham, who have not played since Easter.
"Today, in the key moment at the end of the game, it showed a little bit. I didn't see a winner coming and it is disappointing to concede so late in the game from a set-piece."
Despite the defeat, Wigan are still three points clear of the Premier League relegation zone.