While the margin of victory on Wednesday appeared comfortable, the visitors from the Czech Republic, bottom of Group D with five consecutive defeats, twice fought back from a goal down to draw level before Alvaro Negredo and Edin Dzeko secured the result in the final 12 minutes.
Progression to the knock-out rounds had already been achieved before the victory, but Chilean Pellegrini said he was disappointed with the number of chances Plzen created in an open match at Etihad Stadium.
"I'm satisfied because we won the game but we didn't play well, we didn't play with intensity," he said.
"I think that we can attack and we can score four goals without giving the other team so many chances. 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."
While City have been making headlines for their high scoring, including Sunday's 6-0 thrashing of Tottenham Hotspur, they are six points off Premier League leaders Arsenal, mainly due to defensive lapses that have contributed to four losses away from home.
That carelessness nearly cost them early as Plzen missed two chances before Sergio Aguero scored from the penalty spot after 33 minutes.
City were unable to hold their lead, however, allowing Tomas Horava to score two minutes before the break.
Samir Nasri put the hosts ahead once more on 65 minutes but again the visitors pulled level when a defensive mix-up allowed Stanislav Tecl to level matters four minutes later before Negredo and Dzeko secured the win.
Pellegrini fielded a somewhat second-choice backline featuring Micah Richards, Martin Demichelis, Joleon Lescott and Aleksandar Kolarov and restored England goalkeeper Joe Hart but said it was up to the whole team to ensure control at the back.
"I am not talking about just Richards and Lescott, I am talking about the whole team," he said.
"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."
Hart, who had been replaced by Costel Pantilimon for the club's last four games after a string of high-profile blunders, earned some praise from his manager.
"I think Joe Hart played very well," Pellegrini said.
"I didn't expect that he would have to work so much during the game because I think this is the match when the other team, including Champions League and Premier League, had the most chances to score."