Michael Carrick and Robin van Persie bagged the goals for the visiting side at the Britannia Stadium in a comfortable victory.
The Potters remain just three points above the relegation zone and with only one win in their last 14 matches, they have the unwanted record of being the worst team in the top-flight this year.
Pulis told Sky Sports: "You build up to a big game and you want to play high tempo and everything else and you know you give away a bad goal from a set-play, and that settled United and took the steam out of us.
"Our last two home games against (Aston) Villa and now United, we've given away silly goals."
Asked if it hurts even more when it's a set-piece, he added: "No, they all hurt. It was just a poor goal. I haven't seen it yet but it looked a poor reaction from a couple of our players. Obviously you're going to get quality in when you play the top teams.
"The second goal, the penalty, if Andy (Wilkinson) stays on his feet you've always got a chance. So again, two very, very poor goals for us."