Darren Pratley was clearly fouled inside the area by Luke Chambers when bearing down on goal, but to Sousa's bemusment, nothing was awarded.
The feeling of injustice was made worse by the late winner for the home side, scored by the man who 'fouled' Pratley inside the area and arguably shouldn't have been on the pitch.
The Swans boss told the BBC: "People who make mistakes are only human but what concerns me is that it is happening week by week with us.
"The stadium was in shock when we were not awarded the penalty.
"Everyone could see that it was but we didn't get what we deserved.
"If the decisions in our games had been the right decisions we would be close to the top of the division by now. It's happening too often and I hope someone can explain the situation to me.
"We are a team playing well, always looking to win games and gaining respect from the opposition but there is nothing we can do when we receive decisions like the ones we did.
"But we need to stand up our heads because we need to feel proud."
Sousa's counterpart Billy Davies: "I wouldn't have been very happy if that decision had gone against us.
"But over the last three weeks we've been denied stonewall penalties, so what goes around comes around."