The visitors kept Manuel Pellegrini's men at bay for 70 minutes before Yaya Toure found the net to leave Hughes tasting defeat against his former club.
Stoke created chances themselves and Joe Hart was forced to deny Charlie Adam with a fine stop in the first half.
Hughes felt Stoke were unfairly prevented from testing Hart more often and said: "There were a couple of occasions where I thought - call it professional or cynical - we had good opportunities that were stopped because of my players getting taken out.
"I thought there was a situation - about three or four - when Stoke City players were taken out quite cynically and (that) stopped good situations.
"The ref, in fairness, booked the majority of them but perhaps he could have looked to given another yellow. But what can you do?"
The former Manchester United player was pleased with his team's general performance, but felt they were ultimately architects of their own downfall.
He added: "I was pleased with what we produced. Obviously we had a game plan and when you have a game plan you have to try and execute it to the best of your ability and I thought we did that for the majority of the game.
"We switched off and made a couple of errors, which unfortunately led to the goal. We talk endlessly about consecutive errors and reacting when you see an error in the game.
"We missed a tackle on the edge of the area and allowed a cross to go in. We then didn't track the runner into the box. Consecutive errors usually lead to goals.
"Apart from that, certainly in (the) first half, we were organised and resolute. We kept a very good side in City at arm’s length."
