The Arsenal boss criticized Mike Jones' decision to award the Potters a spot kick following a handball from defender Laurent Koscielny in the Gunners 1-0 defeat.
"It was a nice gift from the referee," he told reporters. "Koscielny is one yard away. He has no time. How can he take his hand away? He has no chance."
The Frenchman also admitted that the defeat was a huge blow in his side's pursuit of the Premier League league title.
"It is a big worry not to win a game like that," he said. "It's a massive setback. We didn't produce the performance that we wanted. To win a title, you have to perform when you're expected to.
"It was a good defensive performance and overall I think we were unlucky to lose this game. Offensively we didn't create enough. Our offensive game was poor considering our standards. At the end of day we didn't score. I don't assess our title chances at all. We just have to play well in the next game."
Stoke boss Mark Hughes disagreed with the Arsenal boss over the penalty, insisting that it was the correct decision from Jones.
"I know Arsenal don't think it was a penalty but I'm a bit bemused by that," he said. "I think it was clear cut to most people.
"They can't have any real complaints. We showed more intensity and drive and determination. They struggled against that."