Match official Mark Halsey did award two spot-kicks in Saturday's 2-2 draw, but waved away appeals for two more after Fulham's Emmanuel Frimpong and Philippe Senderos found themselves in the spotlight.
A frustrated O'Neill said: "It looked a pretty clear-cut penalty from Senderos handling the ball, and the referee has chosen not to give it.
"I suppose it sounds like a bit of a moan and a bit of a rant, but last week (in the 2-1 loss to West Brom) there were two penalty incidents in the game and to me, both were penalties given the directives that we have been given by the referees this season.
"One was given against us and the other one wasn't. The referee chose to miss it, and today again.
"While I agree with the referee that, in general, there are a lot of soft penalties being given, these are the directives we have been given.
"While 20 years ago maybe the game would have not had a penalty at all, the fact is that this is not 20 years ago, it's now, and these are the directives we have been given.
"I keep mentioning that point because it was the referees who mentioned it, so you can't just turn around and give it and then choose to ignore it when you want."