Pellegrini was forced to settle for a goalless draw after a City side showing six changes failed to impose themselves in their latest Barclays Premier League outing.
Stoke even had the better of the game and went closest to scoring when Jonathan Walters headed a good chance wide and Joe Hart produced a good save to prevent a Matija Nastasic own goal.
Stoke manager Hughes said: "I think we are disappointed we haven't won, so that's an illustration of how we feel the game went.
"City have got big games coming up, it is a busy period. Maybe they picked a team they felt could win against us, given the Champions League game in midweek.
"Maybe they prioritised the wrong game.
"They have got a huge squad and you have to use your resources in the right way and get the combination right.
"That is the balance you have to make when you have got riches like Man City have.
"They didn't quite get that right before the game. That probably helped us, looking at the teamsheet."
Stoke have made an encouraging start under Hughes, having performed well in defeat at Liverpool in the opening game and then beaten Crystal Palace and West Ham prior to City's visit.
Source: PA
Source: PA