Mourinho added: "These things are a part of the game, he's playing well for us, he's probably exhausted after two matches with the global team but he can not play Tuesday so is good that he gets his rest and it is an opportunity for Lindelof and [Chris] Smalling".
Mame Diouf (knee) could also return to contention, but winger Maxim Choupo-Moting is doubtful after straining his hamstring while on global duty with Cameroon.
Stoke enjoyed an encouraging start to the first half and put United on the back foot on a couple occasions.
It remains to be seen whether he can be a consistent performer for the Potters this season as he will need to adjust to life in the Premier League, although the early signs are good.
Romelu Lukaku put them ahead in the 58th minute, only for Choupo-Moting to equalise.
Slovakia respects European Union court ruling on refugees, position unchanged - PM
It is part of a scheme to relocate a total of 160,000 asylum seekers by September this year. Slovakia and Hungary challenged the decision.
JOSE MOURINHO WALKED out of a post-game interview with the BBC after he was quizzed about refusing to shake Mark Hughes' hand at full-time. "For us to go toe-to-toe with them, match them in big parts and not allow them as much freedom and opportunity as other teams have given them up to this point, I think we deserve great credit".
The lead was taken by United then lost within six minutes. Stoke's players protested for a foul but what would have underpinned their anger was the knowledge they had conceded so softly and stupidly.
Eighteen minutes from time Mourinho went for the jugular by introducing Martial and Mata for Rashford and Herrera. His initial effort was saved by Butland, but Lukaku's second bite of the cherry saw United score a deserved second goal.
Stoke boss Hughes said: "I pushed him because he was in my technical area. I don't know why he didn't shake hands afterwards, maybe that's why", claimed Hughes to the Daily Mirror. It has to be viewed as a negative result for him. When questioned about it later, Hughes simply laughed it off but Mourinho snapped at the reporter who asked the question.
"I have to say it is a result I accept though".
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