Netherlands Under-21 winger Cissoko was sent off for violent conduct towards Perry Ng.
The Cardiff City defender kicked the ball at Cissoko while he was on the ground after being fouled and he reacted angrily.
The straight red card means he will miss the next three matches against Millwall, Preston North End and Leeds United.
“He’s reacted. Their player’s been quite clever and very dangerous, I feel,” Rooney said.
“He certainly kicked the ball at Ibs on purpose and that could have been a different colour card to what he got.
“But for Ibs he’s reacted in the wrong way and he’s picked up the red card – it certainly didn’t help the team.”
He added: “It’s an opportunity now for someone else to come in.
“Of course he’s disappointed. When you get a red card for something, I’ve been there as a player as well in a similar instance to Ibs’, and sometimes it boiled over.
“It’s not nice when you get that red card like that, he knows he’s reacted to something he probably shouldn’t have and it’s cost him.”
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