Hughes' men seemed to be coasting after goals from Joleon Lescott and Martin Petrov but Roy Hodgson's side hit back immediately through Damien Duff and Clint Dempsey.
The brace stretched City's run without a clean sheet to seven games and Hughes admitted his side's inability to cope with opponents' aerial threat is a concern.
Hughes said: "We were 2-0 to the good and we should have seen the game out but unfortunately we allowed them back in the game and given them a lift.
"Then it was how we dealt with balls into the box and a guy in Dempsey who is acknowledged as good in the air - and we haven't dealt with it.
"We've been caught out a couple of times this season and it seems to be prevalent this year, not just with us but with quite a few of the teams around us. We started really well in terms of our defensive work but we conceded goals and we are working hard on that. There are always elements of our game we need to focus on."