I assume that the England team have the basic details of both injuries and didn't call up Stones because based on that information they don't think he'll be fit to play, and did call up Grealish because based on that information they do think he'll be fit to play.
Pep's not going to have a problem with England assuming John's injury rules him out without asking for more information or input from the club, because the outcome of that is John stays in the care of City's medical team, maximising his chances of speedy recovery (and John might be a bit annoyed to miss the call-up, but ultimately pretty secure in his place in future England squads, so not making a fuss about this one).
But Pep probably does have a problem with England assuming that Jack will be fit to play based on limited information and without seeking out further details from the club, because the outcome is the risk of an injury setback and he knows that, like most or maybe all of our players, Jack's not going to turn down a call-up if it comes.