Villa included a clause in the contract that prevents the 27-year old from playing today when the Potters visit Villa Park.
And Stoke boss Hughes said: "It is one of those things.
"Aston Villa stipulated that they weren't going to allow the loan deal to be changed unless it was in the contract that Stephen couldn't play against them.
"We had to respect that, or we wouldn't have got the deal done.
"It is a shame for us because Stephen was excellent last weekend against West Ham.
"But I think it shows Aston Villa understand what a good player we have got. So you can understand it from their point of view - they don't particularly want to help us."
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