The 31-year-old Spain international, who scored the winning goal against West Ham United to maintain City's eight-point lead at the top of the table, will miss Thursday's UEFA Champions League match against Shakhtar Donetsk and will need to prove his fitness ahead of the match at Old Trafford.
"He was uncomfortable in the last minutes after the goal," Guardiola said.
"We made a test after the game and I don't know if he is able to play on Sunday, so that's why he stayed there, to recover in Manchester.
"It's something, something uncomfortable he felt in the last minutes, before the goal he felt something."
After being asked again, Guardiola said: "Hopefully he can be fit for Sunday but it was too risky to play him (in the Champions League)."
City have nothing riding on Thursday's game having already secured top spot in Group F with five successive victories.
But Sunday is more of a priority with City having the chance to extend their eight-point lead over their closest challengers at the top of the Premier League.