Overwhelming winners against Portsmouth a week ago and brought back to earth by Brighton in the Carling Cup, City were reminded that any side with top-four ambitions need to take on opponents as physical as Wigan and not come away empty-handed.
There were arguments over the penalty that ultimately proved to be Wigan's winning goal after Wilson Palacios was ruled to have been brought down unfairly by Javier Garrido but any sense of injustice should not obscure City's failure to impose themselves enough to make the quality of their football count.
The home side, unbeaten since the first two matches of the season, claimed their second win through goals from Antonio Valencia and Amr Zaki against Vincent Kompany's reply for City. Among City's £70m worth of talent, Robinho was notably well contained. Wigan, quietly proud of an unbeaten record against City that now runs to seven meetings in the Premier League, clearly felt that the best way to extend it was to suppress their opponents' attacking threat by denying them the time and space in which to be creative.
It was a policy that worked and which Mark Hughes, the City manager, was honest enough to acknowledge, even though he insisted that the Wigan penalty was a poor decision on the part of the referee, Steve Bennett, and that his side should have had one of their own, when Richard Dunne went down under Emile Heskey's challenge.
"We felt the penalty against us was a very harsh decision," he said. "Their player was seeking to gain an advantage and dived theatrically. The replays of the other incident show clearly that Richard Dunne was impeded and it should have been a penalty.
"I know referees, like managers and players, are going to have days when they do not get everything right, but all we ask is that they get the big decisions correct and maybe in that respect we should be using video technology.
"But overall we had a lot of possession but did not ask enough questions of the opposition and we need to be better than that."
Steve Bruce, the Wigan manager, saw the penalty for his side as correct, even though he admitted that Palacios had "slightly exaggerated" his fall. He was pleased with Wigan's willingness to scrap. If there was a 50-50 ball up for grabs anywhere on the field there would be a Wigan player straining sinews to be first to it.
There was a lesson for City to learn in that, not least in the manner of the opening goal after 16 minutes when they stood off and watched as Valencia took a couple of touches, aimed for the top left-hand corner and hit the target with a screamer.
Wigan's defending was sloppy for City's equaliser, Olivier Kapo athletically but ineffectively launching himself at Elano's low free-kick from the right, failing to keep the ball out of the six-yard box, where Kompany steered home his first goal in English football. Yet Wigan had been good value for their lead, and were probably not undeserving when it was restored, even though Bennett helped them on their way. His ruling against Garrido was not quite as dubious as the penalty Rob Styles gave Manchester United's Cristiano Ronaldo on Saturday but it did look as though the full-back had done no worse than bring down his opponent by playing the ball.
Zaki scored from the penalty spot, a fifth goal so far from the Egyptian striker, on loan from Zamalek, who has the pace, strength and technique to give Heskey the kind of support he has been missing.
Denied an opportunity to square the scores for a second time, City sensed they would have to find something extra to overcome Wigan's determination and the second half brought a redoubling of their work rate, even though it was not enough to carve out another goal.
Stephen Ireland might have done better after Titus Bramble had carelessly failed to cut out Elano's pass, and Wigan were indebted to their goalkeeper Chris Kirkland for having the reactions to cut out a shot from Shaun Wright-Phillips that he must have seen late. But City were close to being dealt a sucker punch in stoppage time when Zaki, breaking through the middle, robustly resisted the combined attempts of Dunne and Pablo Zabaleta to take the ball from him and was denied a second goal only by Joe Hart stretching to turn the ball over the bar.
Goals: Valencia (16) 1-0; Kompany (22) 1-1; Zaki pen (34) 2-1.
Wigan Athletic (4-4-2): Kirkland; Melchiot, Boyce, Bramble, Figueroa; Valencia, Cattermole (Brown, 52), Palacios, Kapo; Zaki, Heskey. Substitutes not used: Pollitt (gk), Scharner, De Ridder, Kilbane, Koumas, Kamara.
Manchester City (4-2-3-1): Hart; Zabaleta, Richards, Dunne, Garrido; Kompany (Fernandes, 90), Elano (Sturridge, 84); Wright-Phillips, Ireland, Robinho; Jo (Evans, 73). Substitutes not used: Schmeichel (gk), Ball, Ben-Haim, Hamann.
Referee: S Bennett (Kent).
Booked: Wigan Valencia, Brown, Melchiot; Manchester City Kompany, Robinho, Richards, Garrido.
Man of the match: Zaki.