Jim Magilton said: "We defended very well and we were competitive throughout, but we just didn't have enough quality in the final third.
"We passed the ball well and retained possession at times, but our midfield players weren't as positive as they have been and that was disappointing."
Magilton revealed he was sent away from his dugout after complaining about Stoke's multi-ball system, which he said favoured the home side.
He added: "The ball wasn't coming back in quickly enough as we chased the game. I explained this to the referee in a calm and controlled manner, but he didn't do anything about it.
"I just don't think it's fair and something needs to be done about it. It wouldn't happen at Ipswich because I think we do things properly."
Stoke boss Tony Pulis sees his at the top of the table but he's trying to keep his feet on the ground.
"I've been in the game for too long to get too excited yet," he said. "This is a tough league and there is still a quarter of the season to go.
"If we treat the last 12 games any differently than we have the first 34, we will end up with our pants pulled down and have our backsides slapped.
"The players are working exceptionally hard and we have got to keep that up until the last ball is kicked. The back four will get a lot of credit for the clean sheet, but the four midfield players in front of them were fantastic.