Stones picked up a groin injury in a friendly with Belgium which left him absent as City faced Arsenal and Aston Villa in the midst of a title race that came down to the wire, with the Gunners finishing just 2 points behind after 38 hard fought games.
While the 30-year-old did return to play in the Champions League first leg against Real Madrid at the Bernabeu. he only managed just over 10 minutes in the second leg which Guardiola was unimpressed with.
City's centre-back recently brought up Guardiola's reaction to the incident, saying that there is no excuse for breaking an unspoken rule at the club.
“I was never so angry as that moment. Never ever before. I was so disappointed," Guardiola said. "It was a friendly game and we are playing the quarter-finals against Real Madrid, and to win the Premier League. For a friendly game, two players coming back injured...I didn’t like it, at all.
"Before when I was a player the national team manager calls the clubs, now nobody talks. How they feel, how they are. Maybe the physios talk but the managers never.
"In the first or second season with Gareth yes, but now no. Sometimes Ronald Koeman because he is a friend of mine. I know the players don't want to get injured, I always encourage them to go to the national team, it’s a pleasure, but if it’s a friendly game you cannot come back injured."
Guardiola states that friendly games like the one against Belgium hold no meaning and to come back injured from a meaningless game left him furious.
"I’m sorry. If you are focused, if it is a friendly game you cannot come back injured when you are playing the quarter finals of the Champions League, because they put in a lot of work behind (the scenes). They are the first to make a lot of work to arrive in the last stages of the season with a chance to win the titles.
"We are well-paid here, the club pay us, not the national teams. Sometimes you have to respect the clubs. In friendly games you cannot be injured. You can play, absolutely, but you cannot come back injured."