Goals from Joleon Lescott - his first for the club - and Martin Petrov looked to have beaten the Fulham hoodoo but Damien Duff and Clint Dempsey replied to force a 2-2 draw.
Manager Hughes has noted the number of goals coming from set pieces and the detailed analysis will doubtless be passed on to the players who missed a chance to regain a top-four spot.
City’s boss said: “At set pieces we need to do better in terms of positioning and personnel. We’ve been caught out a few times but it’s not just us. Decent balls in are difficult to defend, though that wasn’t the case today.
“We started really well with four clean sheets but we’re conceding now. We’re working hard on that. There are areas we need to focus on and we pick the bones out of the games we have played.”
He admitted: “At 2-0 up we should have seen the game out comfortably but we allowed them back in and we’re disappointed.
The key was Duff scoring, it gave them that boost. If we could have seen it through for ten or 15 minutes after our second goal the game would have petered out and we’d have won
Mark Hughes
“That goal gave them a lift at the right time and then we didn’t really deal with the ball into the box. Dempsey is good in the air - it was a good goal, but I think he was as surprised as most people.
But give them credit - probably the two most difficult games we’ve had here this season have been against Fulham. They get everybody behind the ball, make it very difficult for their opponents, and they keep you on the back-foot with their counter-attacks.”
Fulham boss Roy Hodgson said: “City are getting stronger but overall we felt we deserved a point. Bobby Zamora had an horrific miss, which is a shame because otherwise he was magnificent.
“Mark Hughes wanted to win and took a few risks. Three of our four goals against them in two games were from set pieces, but they are no more vulnerable than any of the other top teams.”