City took the lead twice either side of half time, but Plzen fought hard and pegged back their opponents.
"I'm satisfied because we won the game but we didn't play well, we didn't play with intensity," Pellegrini told the club's official website.
"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 tonight."
City play Bayern Munich in their final group match.