Stones was left out of the starting line-up ahead of the start of Saturday’s friendly against Switzerland at Wembley Stadium.
City explained in a statement that the process of assessing Stones’ injury continued until Monday, before the Three Lions’ coaching staff decided to return the player to his club.
It was decided that the Stones would not play in the friendly match against Côte d’Ivoire on Tuesday and return to his club as a precaution.
City is facing a crisis in its defense line with the entry of the season in recent weeks, as Robin Diach is absent with an injury.
Pep Guardiolas team is competing for 3 championships, the English Premier League, which it leads by a point from Liverpool, and the FA Cup, in which it plays the semi-final against the Reds.
As well as his presence in the Champions League quarter-finals, in which he plays against Atletico Madrid.