Pep Guardiola has been asked to explain his version of events following his post-match conversation with Southampton’s Nathan Redmond.
The Football Association on Friday said it had sought observations from Guardiola, who has until December 4 to respond.
Premier League leaders City won 2-1 through Raheem Sterling’s stoppage-time goal.
Speaking after the match, Guardiola claimed Southampton “didn’t want to play” and “were time-wasting from the ninth minute”.
But he insisted he was praising Redmond despite his rather aggressive-looking manner.
“(I told him) how good a player he is,” Guardiola said.
“Last season he destroyed us here. I didn’t know him last season, I realised how good he is.
“Today he could not attack because they defend all the time, but that is what it is.
“I spoke with Oriol Romeu as well, with (Virgil) van Dijk and with my players as well.”
The Saints forward on Thursday dismissed suggestions that Guardiola insulted him during the on-field rant that came in wild scenes following Sterling’s winner with virtually the last kick of the game.
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Redmond backed up the Catalan’s account of events following reports which suggested Guardiola had in fact been strongly criticising the once-capped England player.
In a statement posted on Twitter, Redmond wrote: “Yes he was very passionate, intense and aggressive but he was only very complimentary and positive to me.
“He commented on my qualities as a young English player and how he wanted me to attack his team more during the game in a similar way to last season.
“I told him I was doing what my manager had asked me to do in the game. That’s it. Nothing negative or offensive was said towards me from Pep and that’s what makes him one of the best managers in world football.
“Losing the game the way we did in the last kick of the game after working so hard for 90+ minutes I was very disappointment (sic) but when one of the world’s best managers compliments you or gives advice in any way, you listen.”
City play West Ham on Sunday at the Etihad Stadium.