Owen Coyle felt his Bolton side played well enough to have at least grabbed a point out of the 2-1 defeat against Wigan.
James McArthur bagged the dramatic late winner for the Latics at the Reebok Stadium.
McArthur followed up a drive by Victor Moses which struck keeper Adam Bogdan and rebounded to the Scot, who could not miss from six yards to secure the points in the basement battle.
Gary Caldwell headed the visitors into the lead just before the break before Mark Davies lashed home a stunning equaliser soon after the hour mark.
And although Ryo Miyaichi was denied by a magnificent save from former Wanderers stopper Ali Al Habsi late on, the visitors held on to secure all three points in the Lancashire derby.
Coyle told Sky Sports: "Of course it's disappointing. I mean, I think that's an understatement to leave it as disappointing.
"I felt in that last 35 minutes we showed our quality and we felt aggrieved, if truth be told, not to have taken something from the game.
"But the first half wasn't good enough, there's no getting away from that. Having said that, it took a set-play goal from a corner when Gary Caldwell was gifted a free header and that's not acceptable.
"The players know who they're designated to be picking up and we needed to get some sort of challenge on the ball.
"We can accept that sometimes you can be out-jumped but not to have a clear header and get no challenge on it. That was poor defensively.
"And even the second goal, which proved to be the winning goal, it's a throw 17 yards from goal and we have two players collide, going for the same ball.
"And then you miss the next header and although Bogdan made a good save from the initial shot, he's looking for defenders to clear the ball but it's fallen nicely for the Wigan lad.
"Having said that, we had a number of opportunities in the second half and we felt that we certainly deserved something from the match."