Speaking after a dramatic John Stones goal sealed a 2-1 win for Manchester City, O’Neil expressed his frustration about the decision not to overturn the goal which many feel should not have been given due to Bernardo Silva standing in front of goalkeeper Jose Sa.
"There's no chance people are purposely against Wolves, let's be clear," he said. "But is there something in the subconscious around the decision making - without even knowing it are you more likely to give it to Man City than Wolves?
"My senses are heightened when we are facing Man City, are the officials the same? When it's (Erling) Haaland and Man City is there something in there that, not on purpose, influences decision making?
"They guarantee me there isn't. But they are human and Man City scoring a last-minute winner is a big thing, a bigger thing than Wolves scoring a last-minute goal against West Ham.
"If I had to upset someone in the street and there's a big and little guy in the street, I'm upsetting the little guy."
The FA will now speak to O’Neil about his comments and he will have to explain his remarks in detail or face punishment.
The Premier League's match centre posted on X about the incident and their decision not to overturn the goal.
"The VAR deemed Bernardo Silva wasn't in the line of vision and had no impact on the goalkeeper and recommended an on-field review. The referee overturned his original decision and a goal was awarded."