Aguero disputed Massey-Ellis's decision to award a throw-in to Arsenal during the first half of City's 1-0 win at the Etihad on Saturday evening.
The Argentine, who was making his first City appearance since June after undergoing knee surgery, was unpunished but faced criticism on social media for his part in the incident.
Micah Richards, a former team-mate of Aguero's at City, said the 32-year-old "should know better" and Aguero was also censured by Match of the Day pundit Ian Wright.
The laws of the game state that any "physical or aggressive behaviour" against a match official is considered to be a sending off offence.
Guardiola however played down the incident, insisting that Aguero's actions were not aggressive.
"Come on guys. Sergio is the nicest person I ever met in my life," the City manager said. "Look for problems in other situations, not in this one."
Aguero played 65 minutes on his return to the City side and had a hand in Raheem Sterling's decisive goal, which saw Guardiola overcome his former assistant Mikel Arteta.