The hosts opened the scoring through Gary Hooper's deflected strike, but Pajtim Kasami levelled before the vibrant visitors won it through Scott Parker's late strike.
"We'd built a little bit of momentum. We're a bit like that. Once we make a
couple of steps forward it's a step back today. It's tough at the moment. We're tested in that midfield area with the injuries we have,'' said Hughton.
"We got the goal and had two other very good chances, but conceded a very poor goal just before half-time that gives them a lift.
"We got a lot of balls into the box, but they're a good side with good players. The game became a little bit open and they capitalised on that.
"It (the result) was hard to take. We knew how they were going to play and had to be mindful of being caught on the break.
"We didn't start so well but then got into a real good rhythm. We got the goal and had another good chance through Johan (Elmander) and in that period I think we needed to get a second goal.
"But we conceded a poor goal which gave Fulham a lift and the second half became open and end to end, but I thought we threatened in the final third.
"On the balance of play and the balls we got into the final third, I think it's a game we should have won."