Barkley is fancied by many to be part of Roy Hodgson's 23-man World Cup squad on Monday, with Stones an outside bet to feature, but both players remain eligible for Gareth Southgate's age-group side should they be overlooked.
"There were three players I had to protect today, Ross and John were two and Antolin Alcaraz was the third," he said.
"(Barkley and Stones) will be busy. There is always the opportunity of representing the senior side but not there is the Under-21s and the Toulon Tournament.
"In one way or the other they are going to be busy and that is one of the reasons we had to look after them, to make sure they didn't go into the summer with the risk of an injury.
"You get so many stats these days, so much information on how the body is recovering and sometimes you get a clear indication of a body having a bit of risk of injury; today I wasn't going to take a risk with any of these players."
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