Monday's 1-0 fifth round defeat at the DW Stadium was like a repeat of the 2012-13 final match won by Wigan when the Latics were in the top tier.
Television pictures appeared to show a home supporter and Aguero involved in a physical exchange.
Wigan chairman David Sharpe told BBC Radio 5 Live: "Probably, we will get in trouble".
"It's brilliant - obviously it was a nice easy game out there", Grigg said with jest. Stay with us throughout the day for more as we prepare for Sunday's Wembley showdown. "I don't like what I am seeing here".
Guardiola, who said his side "gave absolutely everything", refused to comment in detail about the red card, and his subsequent clash with Cook.
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That only increased when referee Anthony Taylor, a yellow card already in his hand, reached for the red.
The result marked the end of City's bid for four trophies this season, and Guardiola played down the significance of the red card.
Guardiola said: "Nothing happened in the tunnel, nothing happened with my colleague".
Will Grigg bagged the victor 11 minutes from time to earn Wigan a third quarter-final in six seasons at home to Southampton.
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. I don't think Pep and his bench thought it was but that's football. We conceded one shot on target in 90 minutes and we lost. The scenes were reminiscent of those at Ashton Gate when Bristol City beat Manchester United in the Carabao Cup in December. "Congratulations to Wigan", added the Spaniard, whose side enjoyed 82 percent of possession in the second half.
After the final whistle hundreds of home fans invaded the pitch while City's players moped toward the changing room. "From our point of view we are trying to get every edge and everything we can, and from his point of view he wants the game played and he is a fantastic manager". "They have let in 20 goals in the Premier League this season, a total only bettered by Manchester United (19), and have also kept the third-highest number of clean sheets (12) behind Chelsea (14) and United (15)".