The England defender has started less than half of City’s Premier League matches, though has featured in 18 games in all competitions this campaign.
The City boss was asked during his pre-West Ham press conference whether Stones’ Euro Championship prospects were a concern for him and Pep responded: “It’s my problem.
“I am a human being; I suffer when they suffer.
“I want John to be with the national team. My feeling for him is the same as always.
“I have to make decisions and be honest. It’s not easy when I select Eric Garcia (ahead of Stones), but he played really well and deserved a chance.
“It’s not about a particular reason (that he hasn’t played as often).
“Not just John, but all the players can be selected for national teams. They have to play here as best as possible.”
The boss also commented on some of the more confusing rule changes that have come into effect this season.
Earlier in the campaign, if a keeper was off his line when a penalty was taken, it had to be retaken.
Hugo Lloris was clearly off his line when he saved Ilkay Gundogan’s spot-kick at Spurs – but Pep says that law seems to have changed.
“In Champions League, if they are off their line, that would be disallowed,” he said.
“But here there is a new rule. Here keepers can go forward and not have a save disallowed.
“In one country it is one way, and another it is different. I am not in meetings but the people told the guys in Europe it is different to here.
“The rule is the same for everyone here.
“What’s confusing is why it is handball in one game and not another.
“We believe VAR is going to help because machines can make mistakes. But of course, people use the machines..”.