The Potters have a reputation for being a side difficult to breach from dead-ball situations, while offering a considerable threat at the opposite end of the field, but they were undone on three occasions by the Gunners at Emirates Stadium.
Hughes admits it is unlike Stoke to be hurt in such situations, but feels his side offered enough in north London to suggest there will be better days to come.
He told Sky Sports: "Obviously we're disappointed to have lost three goals from set-plays.
"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."