Juan Mata, Daley Blind, Ander Herrera, Ashley Young, Luke Shaw and Sam Johnstone have just a season remaining on their United deals, but the Portuguese points to the one-year extension clauses included within them.
United had been flying in their opening three games of the season, and Mourinho was quick to blame the global break for disrupting his team's rhythm.
"A number of the others came back with little niggles but they won't be the type of injury to stop players playing".
After a few minutes they scored their goal, which I'm not happy with especially, because after a great save (from David de Gea) as a team we have to defend that corner.
Mourinho refused to be drawn on the reasons why he refused to shake the hand of Hughes at he final whistle, as he offered up these comments after the game.
"I seem to get involved in "Handshake-Gates", Hughes joked. "I'm really grateful for the second opportunity".
And while the United manager says his side are capable of following that example, he also wants to ensure they play in a positive fashion.
"It's a negative. Sometimes managers of top-six clubs don't take negative results too kindly".
Mourinho's team had their flawless start to the season dented by Mark Hughes' men at the Bet365 Stadium where United have not enjoyed recent success. "He knows the mistake, part of his game is playing well for us, but he was probably exhausted after consecutive matches with the national team".
Geoff Cameron, left, came out of Stoke City's game against Man United after the first half.
Team to play Manchester United: Butland, Cameron, Zouma, Wimmer, Diouf, Fletcher, Allen, Pieters; Shaqiri, Jese, Choupo-Moting.
When commenting on the first goal he said: 'It was a wonderful cross for their opener but Bailly could have done much better.