Jack Butland was beaten in the 77th minute by a fine David Nugent header, which made it a slightly uncomfortable finish to the game for Stoke, who had taken a two-goal lead through Kenwyne Jones and Charlie Adam.
Hughes said: "Collectively we were good today. It was important that we paid the competition and the opposition the right level of respect and I thought we did that.
"I was able to go quite strong. I thought it was important to pick the same back four because Jack hasn't played too often with them. It was important he had the benefit of that because he's going to be in goal for a couple of weeks I would suggest.
"I wanted to give Kenwyne a run-out because he's been very patient, and he hasn't played because Peter Crouch has done very well for me. He's come in and acquitted himself very well, got a good goal and could have got a couple more.
"Charlie once again has had an effect on the game in a positive manner, scored a great goal and could have had another one."
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