There were fears Bentley could be frozen out after he controversially elected to withdraw from the summer squad for the European under-21 Championships because he said he was too tired.
But Hughes insisted: "We have drawn a line under it and there is no real issue between me and Steve [McClaren]. I was delighted when he rang me this morning to tell me David was in the squad.
"He scored a brilliant goal for us on Thursday night but I would suggest it is his form over a sustained period of time which has probably swayed it. This is David's reward for a lot of hard work."