Arsenal striker Olivier Giroud in particular was on the end of some rough-looking treatment during the game, with Stoke midfielders Glenn Whelan and Charlie Adam appearing to stand on the France international.
Wenger after the match made reference to the Potters' physicality, but was reluctant to speak about individual incidents.
He said: "You have to give credit to Stoke. They defended well, with resilience, and made the game very physical.
"We knew that would be the case before the game, though. They have the highest number of fouls in the Premier League. But we didn't cope well enough with it and at the end of the day we were punished."
Asked about the challenges on Giroud, Wenger added: "I don't want to talk about the referee. I have nothing to say about that.
"I am long enough in the game to make my own judgement and I prefer to concentrate on our own performance."
When questioned about Adam in that context, Stoke manager Mark Hughes said it was the first he had heard about it, adding: "It would be a shame if people highlight that as it wasn't that type of game."
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