The City star was summoned in the 41st minute against Atalanta when Rodri picked up an injury.
But Guardiola was visibly riled during the 5-1 Champions League victory with Stones not ready to come on.
“The guys on the bench know you have to be ready to go out from the first minute,” Guardiola explained.
“Sometimes it’s the t-shirt or other issues. Did you see the image? So it speaks for itself.”
As well as Rodri, who is out until the next international break, Guardiola has lost Oleksandr Zinchenko for six weeks with a knee injury, leaving the Blues boss short of options.
“We are in a bad period in that sense,” said Guardiola.
“I’m a little bit concerned because in a few positions we don’t have enough players.
“I would prefer all the players had no injuries but I have to do it, yes. We can’t start complaining, ‘oh what bad luck.’
“We have good players in the squad. In a few positions there are not many but we have incredibly good players. We’re going with them.”
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