The Potters protested in vain after the referee pointed to the spot once in each half which resulted in two goals for the home side, both penalties were converted by Javier Hernandez and Dimitar Berbatov.
The first one came about when Jermaine Pennant tripped Ji-Sung Park just before the half-time break, the second was a result of Jon Walters bringing down Antonio Valencia just after the restart.
Pulis fumed: "Jermaine is adamant, although it doesn't show it on the television, that he played the ball first.
"On the second, it's not a free-kick before the penalty. Then Valencia runs across Jon Walters and falls over.
"When you come to Old Trafford, if there's decisions going, they go with the home side."
In actual fact, there was another incident in which United should have been given another penalty, but we won’t go into that for fear of Mr Pulis blowing up with rage.
He pointed out that Stoke came to Old Trafford to have a good go at United as they were sick of being beaten here, he was looking for their first win in four visits since they came back up to the top flight.
But to be honest, if that was Stoke giving it a good go, then tey are in big trouble what with their negative, defensive display looking for a 0-0 draw. I’m glad I don’t have to watch this sort of football every week.
"That's the first time we've come here and played with four forwards," he went on.
"We wanted to give it a go and put players on the pitch that would give us a chance.
"I wanted to see what we could do with four up against them, but it's keeping the ball and having that belief. It's disappointing that final pass or final decision wasn't as good as it has been.
"But United were very good at times. They are a top team and you have to give credit to them as well. And the penalties don't help. The decisions have gone against us."