With his team trailing the Potters by a single goal heading into added time, the Royals boss is convinced Adam Le Fondre was fouled by Ryan Shotton inside the area only for referee Michael Oliver to disagree as the relegation-threatened outfit headed home empty-handed.
"Once we got to 2-1, I thought we would get [a draw], and unfortunately the ref has missed a penalty at the end, the last kick of the game," he told reporters.
"He got hold of the ball, flicked it by him and he caught him. It was a stonewall penalty. I've just gone in to see [Oliver] and he didn't see it that way, so that's fine, but I thought it was.
"Sometimes as a manager you get those things - with the last kick of the game, it would have been great to get the point."
Tony Pulis, meanwhile, dismissed the incident and insists even if Shotton did foul the Le Fondre his side deserved a break regardless.
"It has been a long time. I thought we deserved to win the game - I would have been absolutely devastated if we hadn't won the game today," he told reporters.
"Firstly I was told it was a penalty, then I've just been told it actually isn't from a different angle - that the lad isn't caught, but just arches his back and falls over.
"It will be interesting to see, but if it was a penalty, I have to say thank goodness we have had a break, because we deserve one."