Gary O'Neil expresses his frustration to the assistant referee after Manchester City's winner.Photograph: Tim Keeton/EPA

The Wolves manager, Gary O'Neil, questioned whether referees have a subconscious bias in favour of the "big guy" after Manchester City clinched a stoppage-time victory in controversial circumstances.

John Stones scored a 95th-minute header from Phil Foden's corner to extend City's unbeaten run to a club-record 31 matches but Bernardo Silva made contact with the Wolves goalkeeper, Jose Sa, as the ball was en route into the box. Wolves are aggrieved because it was near identical to when they had an equaliser ruled out against West Ham last season.

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The referee, Chris Kavanagh, initially disallowed City's goal because his assistant Constantine Hatzidakis raised his flag for offside against Silva. The Premier League said the VAR, Stuart Attwell, deemed Silva "wasn't in the line of vision and had no impact on the goalkeeper and recommended an on-field review". For Wolves, who voted at the end of last season against the use of VAR, it was another frustrating episode. "The referee overturned his original decision and a goal was awarded," the Premier League Match Centre said.

O'Neil made clear the referees act in good faith but said other factors could influence the officials. "Is there something in the subconscious around the decision-making?" he said. "Without even knowing it, are you more likely to give it to Manchester City than Wolves? My focus and senses are heightened when we're facing Man City, Pep [Guardiola] and [Erling] Haaland. Are the officials the same when it's Haaland and Manchester City? Is there something in there, not on purpose, that influences decision-making? I've spoken to them about this and they guarantee me there isn't, but they are human.

"I can categorically tell you that they definitely don't mean to. I just know from a human point of view, it's tough. If I had to upset someone in a street and there was a little guy and a big guy, I'm going to upset the little guy. Maybe there is something that edges it in that direction when it's really tight."

O'Neil said the decision to allow the winner was "a tough blow", particularly given the parallels with when Wolves had a 99th-minute equaliser at West Ham disallowed in April in similar circumstances; then the Wolves forward Tawanda Chirewa was deemed to have obscured the view of goalkeeper Lukasz Fabianski.

"We sent an image to referees showing with proof that the West Ham keeper could see the ball, but the reason we were given was the player [Chirewa] was in close proximity," O'Neil said. "The same argument could be said here but we just have to accept it."