Footage showed the Argentine raise his hand after being taunted by a Wigan fan before he was led off the pitch by City staff.
ESPN's Jonathan Smith summed up the feeling of shock many felt with his post-match analysis, describing the result as "incredible".
Thoughts on last night's bust-up between the Manchester City striker and a fan?
Journalist Jose Alvarez Haya told ChiringuitoTV: "A fan spat at Aguero and Kun feared he might have an object to cause him harm".
The Premier League leaders were stunned by the League One side in the fifth round.
Guardiola was furious with that decision and Cook drew his ire as the pair exchanged heated words on the sideline.
The goal was his seventh in this season's competition, more than any other player, and ended City's hopes of an unprecedented league and cup quadruple.
Manchester City suffered a blow yesterday, as they travelled to DW Stadium to square off with Wigan Athletic.
Wigan stopped City's quest of winning the FA Cup a second time beating the Citizens in the final of 2013 despite being relegated to the lower tier of English football.
Guardiola said: "I was in the locker room, I didn't see it".
"It was a big night, as you could see the fans were on the pitch at the end, which I personally don't like seeing for any team."
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"It's not nice to see", said Wigan chairman David Sharpe, who committed to investigating the incident.
Plastic bottles, coins, and advertising hoardings were all used as missiles as the home fans flooded the pitch.
Stewards and the police struggled to contain the situation as it got out of control.
Referee Anthony Taylor initially pulled the yellow card out of his pocket and then appeared to change his mind, with Guardiola reacting furiously.
Cook was reluctant to go into the incident or its aftermath, saying: "I think we should speak about the game". There were four people there with the fourth official. It can be a red card. "The referee decided what he decided". It can be a red card. Nothing happened in the tunnel.
"It was just "please stay in your position".
"I don't have regrets with the way we played, the performance, the heart".
"If anything, the dismissal just before half-time inspired City to cause Wigan even greater problems following a decent first half in which they should have been ahead".
"From our point of view we're trying to get every edge in everything we can", Cook said.