Sharpe: I don't like to see this at end of a game
Fans spilled on to the pitch at the DW Stadium as the hosts celebrated their 1-0 fifth round win against the runaway Premier League leaders.
Supporters from both clubs were involved in disturbances, while television pictures appeared to show a home supporter and striker Aguero involved in a physical exchange.
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Hide AdAdvertising hoardings were ripped out and thrown and a pitch invasion by Wigan fans got out of hand while the defeated City players were being escorted off the pitch.
Video footage also appeared to show objects, including an advertising board, being thrown at police officers by fans in the City end.
Wigan chairman David Sharpe said: "It is not nice to see, football is emotional, it is what it does to fans. But I don't like to see this at the end of the game.
"It is a massive result, but we have to stay classy in football, I don't like what I am seeing here".