Southampton dominated for large periods and turned the game around to take the lead after 86 minutes, Schneiderlin himself finishing off a fluid counter attacking move.
However, just three minutes later Shaun Maloney equalised for Wigan to rescue an undeserved point for the home side.
"We should have had the three points. We came here with the intention to win the game and did everything we could to do so," Schneiderlin said.
"We are disappointed that we have conceded two goals from corners, because from open play you couldn't see how they could score.
"In the last minute to concede a goal like that is disappointing.
"Still, we keep them three points behind us and we are going to try to make that a bigger gap over the next few games."