Hughes claimed his side had had a penalty wrongly given against them and been denied a clear one themselves in their 2-1 loss to Crystal Palace.
Referee Andre Marriner adjudged Asmir Begovic to have fouled Yannick Bolasie, who was chasing a long ball forward, as the pair collided in the box and awarded a spot-kick which Glenn Murray firmly despatched.
The official also booked Begovic, but Hughes felt it was Bolasie who had been guilty of an infringement.
The Stoke manager said: "My take on it at the time was that is was just a long ball knocked forward, and maybe we hadn't dealt with it as well as we'd like to.
"But then you see the replay and you understand why, because I thought the lad Bolasie has got his foot up high, and that is what has taken Asmir's eye and why he has missed the ball.
"The referee deems it a penalty, but in my view it was a free-kick the other way for dangerous play.
"That was the key moment and those are the big decisions you want referees to get (right). Andre Marriner missed a lot of things today I felt."
Hughes was also aggrieved about an incident midway through the second period - by which point Stoke were trailing to Wilfried Zaha's goal in first-half stoppage-time - when a Diouf shot in the area struck the arms of Palace defender Joel Ward, with play being allowed to continue.
Hughes said: "It was clear - arguably it was the best save of the match!
"(Palace goalkeeper Julian) Speroni has done great, but that was a full-length save (by Ward) and he has two hands on it, for goodness sake. How he (Marriner) doesn't give that penalty is beyond me."