Stones' only action this season has come for England, playing twice in last month's internationals before starting against Andorra on Saturday.
Southgate said: "I don't foresee it being a problem, he's just been really unfortunate.
"He got a niggle at the start of the season just before their first game, and I know looking at how it worked, he was on the bench after coming back from us, then got injured in training the day after.
"Then going into that last run of three games, a lot of the big managers, when they are in games like that, playing a team who are up to speed physically, will be thinking about not changing.
"For those three games we probably knew that would happen.
"John, when he goes back, will have that many games and everybody knows his quality, so he will be in the team and I don't think that will be an issue going forward."
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