The Chilean made six alterations to his side for the clash at the Britannia Stadium, a move which the Welshman believes upset the balance of the team
Last season's runners-up struggled for fluidity and laboured to a goalless draw against Stoke on Saturday.
Hughes believes Pellegrini didn't get his squad balance right following a string of alterations to his squad, which allowed Stoke several chances to secure three points.
"They've [Manchester City] got a huge squad and have to use your resources in the right way and get your combinations right," Hughes said.
"That’s the balance you have to make when you've got the riches Man City have.
"Maybe they didn't quite get that right, before the game that probably helped us looking at the team sheet."
"I thought in terms of chances created we certainly had the better of those. Probably the only thing missing was the ability to convert a chance.
"Overall we're happy with the performance, if we keep our performances at that level then we'll have a good season.
"Our performances have improved steadily, and we've got to maintain it."