Second-half goals from Antolin Alcaraz and Victor Moses capped a convincing display against an out-of-sorts Stoke.
Pulis also had no complaints over the tackle from Emmerson Boyce which led to the winger's withdrawal after half-time.
He said: "I'm more upset with the way we played.
"I thought Wigan were the better team, they played better on the day. It's very difficult for me to be critical of the team and the players because we've done so well lately and we've had a real tough run of games.
"There's incidents in every game you can pick out but it doesn't take away from the fact Wigan deserved the three points."