Hughes was not happy with all of City's tactics, feeling that some of the home players pushed the boundaries of legality.
Vincent Kompany - a player Hughes signed for City - was one player Hughes commented about.
He said: "I thought on a couple of occasions - call it professionalism or good play, or a bit of cynical play - we had good opportunities that were stopped because my players were being taken out.
"The player that you mentioned and on three or four other occasions Stoke players were taken out quite cynically in my view.
"It is part of the game and the ref, in fairness, booked the majority of them but maybe he should have looked to give another yellow card."
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