The Potters went down 3-1 to Arsenal at the Emirates Stadium with Hughes slightly critical of his players for allowing the Gunners to hit the back of the net through Aaron Ramsey, Per Mertesacker and Bacary Sagna all from Mesut Ozil dead ball situations.
"Obviously we're disappointed to have lost three goals from set-plays,” he told Sky Sports.
"I don't think Arsenal over the years have scored many goals from set-plays, certainly not three in one game. Against us it's more galling, I think.
"Yes, we're disappointed but we certainly made a right fist of it and I think we tried to get the ball down, passed and moved and tried to pull them out.
"Just prior to their third goal I thought we had total control of the game and they looked tired, given that they had a tough game in midweek. I thought we created opportunities.
"As it was, the third goal really knocked the stuffing out of us and it was very difficult for us to get back on terms then. But I thought up to that point we were always in the game and playing the right way."