There is a famous song about the man who has just scorched Manchester City’s hopes of a quadruple. And in the closing moments here it is doubtful if “Will Grigg’s on fire” has ever reverberated around this stadium with greater noise and fervour. City were on their way out of the FA Cup and once again it was Wigan – little, patronised Wigan – who had left the most expensively assembled group of players in English football history on their knees.

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They will cherish Will Grigg’s breakaway, 79th-minute winner here with almost as much fondness as that never-forgotten moment when Ben Watson’s header in the 2013 final gave Wigan the greatest victory of their history. Grigg is now the leading scorer in the competition with seven goals and Wigan, having already beaten Bournemouth and West Ham, have become only the second team from outside the top two divisions to knock out three top-flight clubs in one FA Cup campaign since the second world war. Southampton are next in the quarter-finals.

That made it a wretched night of humiliation for City and Pep Guardiola, one imagines, will not take any consolation from the fact he had repeatedly warned everyone he did not think it possible to win four trophies in one season.

City have a 16-point lead at the top of the Premier League and are virtually guaranteed a place in the Champions League quarter-finals, with the Carabao Cup final against Arsenal on Sunday. Yet their manager looked almost as frazzled at the end as Roberto Mancini had at Wembley five years ago.

The only downside of a glorious night for the third-placed team in League One came after the final whistle when Sergio Agüero, swapping shirts with Chey Dunkley, was goaded and attacked by a Wigan fan before losing the plot and trying to go after the aggressor. Agüero had to be chaperoned away, with Dunkley trying to stop it getting out of hand, and when hundreds of pitch invaders started goading the away fans it was almost inevitable there would be a reaction. Police reinforcements had to be called as things quickly escalated. Missiles were thrown by both sets of fans and City’s supporters could also be seen pulling down the advertising boards to hurl them on the pitch.

The Football Association is bound to investigate and it is also possible City will face disciplinary action because of the way their players crowded round the referee, Anthony Taylor, to remonstrate after Fabian Delph’s red card late in the first half. As Paul Cook, the Wigan manager, pointed out afterwards, Delph’s dismissal made a considerable difference and Taylor did not help himself by initially pulling out a yellow card.

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Something clearly changed his mind about the severity of Delph’s flying challenge on Max Power. It was a strange set of events, to say the least, and Delph’s team-mates were probably entitled to suspect the referee had been influenced by the reaction of the Wigan players.

Guardiola insisted afterwards that he agreed with the sending-off although his reaction at half-time, when he confronted Taylor in the tunnel, and another angry outburst afterwards indicated those might not have been his true feelings.

Neither he nor Cook wanted to discuss the argy-bargy in the tunnel at half-time. Yet Cook, his voice hoarse with emotion, had a nice line when he was asked to describe the nerve-shredding moments when City poured forward in search of a late equaliser. “Shut your eyes and pray,” the victorious manager explained.

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In many ways this was actually a greater shock than 2013 bearing in mind Wigan, now two divisions lower, had also lost their most creative player, Nick Powell, to a first-half injury.

Yet even when the two sides had equal numbers City had looked strangely out of sorts inside a ground where the advertising boards promote Uncle Joe’s mint balls and Ribble Farm fruit and vegetables. City always look more vulnerable when Claudio Bravo is in goal. Danilo, selected ahead of Kyle Walker at right-back, was particularly accident-prone and Wigan must have been encouraged by the space when they did venture forward.

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Guardiola had given Ederson, Raheem Sterling and Nicolás Otamendi the night off, with Kevin De Bruyne restricted to a substitute’s appearance, but City still had enough mega-money signings on the pitch to have done much better.

Their two centre-backs alone cost well in excess of £100m and it was noticeable that Guardiola did not defend Delph for what was a silly and risky challenge. For his troubles Delph will be suspended from Sunday’s trip to Wembley.

Cook had joked beforehand that he was applying for special permission to field 14 players. As it turned out, his side had the numerical advantage through unforeseen circumstances. Wigan still had to defend for their lives and for long spells City’s 10 men still dictated the pace and tempo in the second half, with Danilo and Walker often playing as auxiliary wingers.

But then the ball was aimed through the inside-left channel and Walker, a half-time substitute, did not react quickly enough. Grigg still had a lot of ground to cover before he was inside the penalty area but he took his shot early, Bravo never likes having to dive and Wigan, incredibly, had done it again.