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 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.
Hughes is trying to change perceptions of Stoke as a physical and direct team and his influence was evident as they played the better football throughout.
Hughes said: "In terms of chances created I thought we certainly had the better of those.
"It was probably the only thing missing from our performance, the ability to covert a chance. We created enough of them.
"But overall we are happy with our performance. If we keep our performance at that level we will have a good season.
"Our performances have improved steadily as the season has gone on.
"It is still early days, so we have got to maintain it but we have got a lot of confidence because what we are trying is working."
Hughes refused to criticise Walters, who glanced his headed chance wide after being picked out by a fine cross from the superb Charlie Adam.
He said: "I've been a striker, I have been in those situations - do you let the ball just hit your head or do you try to guide it?
"Sometimes they come off, other times they don't.
"Unfortunately it just went past the far post but I thought Jon was great. He put in a real shift for us and was unlucky."
- Sports & Recreation
- Barclays Premier League
- Jonathan Walters
- Matija Nastasic