Hughes suggested Manchester City may have paid the price for taking Stoke too lightly after the Potters frustrated Manuel Pellegrini's men at the Britannia Stadium.
He 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."
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