The Citizens were twice pegged back by the Czech outfit, but eventually prevailed 4-2 at the Etihad Stadium last night.
City have now conceded two goals in each of their last three European games, and the Chilean believes that the problem lies with the whole team and not just the backline.
"I'm satisfied because we won the game but we didn't play well, we didn't play with intensity," he told reporters.
"One of the most important things to being an attacking team is knowing how to defend and I think on that front, we did very bad.
"I am not talking about just [Micah] Richards and [Joleon] Lescott, I am talking about the whole team. The whole team must know how to defend. We didn't have the intensity or the pace today to do it and I am not talking about individual players."
A trip to the home of reigning champions Bayern Munich awaits City in their final match of the Champions League group stage.