Shotton has returned to Stoke after his loan spell at Wigan Athletic.
"Ryan went out to Wigan because there was an opportunity," Hughes told The Sentinel.
"I was happy to do that to give him games because I felt that initially he wouldn't be playing much here.
"When there was a change of manager (at Wigan) that affected him.
"The feeling up there was that there was a lot of players at Wigan and the new manager is going to concentrate on the players who were going to be with him for the whole season.
"But now he is back here and available to us."
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