George Boyd drove in through a crowded penalty area to set up a tense finish but earlier second-half goals from Ross Barkley and Miguel Llera ensured the Owls leapfrogged their opponents.
"I said at half-time that I think we got caught in a bit of a trap because of the way they played," Ferguson said.
"We were in control of the game I felt, they didn't cause us any problems really but I just think we seemed content to play at a tempo that suited them.
"I don't know if there was enough conviction about us in the first half which disappointed me more than anything really.
"We knew Barkley ran on from flick-ons and we didn't deal with it. Then we got control of the game again possession-wise and we've lost a poor second and I thought when Boyd scored we would get something out of it.
"I don't think it was a game we deserved to lose.
"But we've put ourselves in a position where virtually every game is a cup final because we've had such a poor start to the season."