The defender was missing for the win against Sunderland on Saturday.
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Afterwards, manager Pep Guardiola confirmed Stones was absent due to injury. Asked for a timescale on his return, Guardiola admitted "I don't know..."
The Manchester Evening News says Stones is a 'significant doubt' for the clash at Real Madrid on Wednesday night.
Meanwhile, midfield pair Rodri and Mateo Kovacic won't be seen until the New Year.