Hughes' men fell behind in the first half through Jonny Howson's long-range strike and never really threatened an equaliser as they slipped to their first home defeat of the campaign.
However, Stoke were left aggrieved in the early stages of the second half as Kenwyne Jones was pulled back by Leroy Fer in the penalty area.
And former Manchester City and Wales boss Hughes believes that referee Anthony Taylor should have pointed to the spot, but accepted that Stoke's performance had been disappointing.
"We were below par today," he said.
"This is a Premier League game and we need players to perform and we haven't.
"It's only today that they have let themselves down, it was a disappointing performance and we were poor. We never got any pace or power into our game which is unlike us.
"If the referee sees it, he will agree there is an infringement, Kenwyne Jones was trying to get on the end of the ball, the letter of the law says it should be a penalty.
"But we needed to be better today but they were comfortable when they got the goal and overall we were well below it."
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