Play was halted when Walker marched over to referee Jarred Gillett before taking a throw-in seemingly furious at the Bees forward.
Gillett then had a conversation with Maupay, who cut a confused figure as he looked back in Walker's direction.
It's not clear what was said between the two but City vice-captain Walker was seen being calmed down by Guardiola as the exchange unfolded.
Maupay was substituted in stoppage time by Brentford boss Thomas Frank amid more troubles with the French forward.
The 27-year-old was also seen speaking to Guardiola after the final whistle was blown.
READ MORE ON MAN CITY
Premier League fixture amendments has bizarre new kick-off time for Liverpool vs Man City
Guardiola wasn't looking when Toney found loophole for Brentford goal against Man City
This is far from the first on-pitch controversy involving Maupay, who got into a spat with James Maddison during Brentford's defeat at Tottenham last week.
Having mimicked Maddison's darts celebration after putting Brentford in front at the Tottenham Hotspur Stadium the duo were seen getting into a heated discussion which looked like it was going to spill into a physical confrontation.
Maupay and Maddison then exchanged jibes on social media after the match.
It was a good Monday night for City as they secured a 3-1 victory over Frank's side to go just two points behind Premier League leaders Liverpool.
Most read in Football
Lisandro Martinez ruled out until at least April after Man United star's injury setback
Mauricio Pochettino not in immediate danger of being sacked as Chelsea boss
Premier League fixture amendments has bizarre new kick-off time for Liverpool vs Man City
Joe Worrall set for Nottingham Forest exit despite transfer window being shut
But they endured a bad start when Maupay put Brentford in front with a cool finish after City failed to clear Mark Flekken's goal kick.
Phil Foden got their equaliser just before half time and his header and composed effort saw him net a hat-trick in what was a virtuoso performance from the England star.