That goal was number 174 in the Premier League for Aguero, making him the highest goal scorer in the league this decade.
Guardiola clinched his 100th win in charge of the team after 134 EPL matches - beating Jose Mourinho's previous record of 142.
Sheffield United's Lys Mousset had a goal disallowed by VAR for a marginal offside and referee Chris Kavanagh also accidentally impeded a visiting player in the buildup to Aguero's goal.
"I said many times that I have a huge list for VAR".
Sergio Aguero opened scoring for the Citizens in the 52nd minute after firing a thunderous shot into the roof of the net with Kevin De Bruyne claiming the assist for the opener.
Wilder said: "There's no conclusive evidence, blurred lines and angles".
In the first game of the city, Wilder added that he is convinced that a mistake was made and that the referee should have made the "sensible decision, quot; to reject the goal".
"If he had made the sensible decision, then I don't think anyone on the ground would have said anything about it".
Any hopes of a comeback were ended soon after as De Bruyne calmly swept home, though Billy Sharp went agonisingly close to setting up a grandstand finish with a looping header which hit the upright and rolled across the line as United's unbeaten run on the road came to an end at nine. "Hopefully next season it can do better", Guardiola said.