Pep Guardiola's runaway Premier League leaders had their prospects of an unprecedented quadruple ended by League One Wigan Athletic on Monday, with Will Grigg firing a 79th-minite winner at the DW Stadium after the visitors had Fabian Delph sent off.
Delph's red card sparked an angry confrontation between both benches, with Guardiola and opposite number Paul Cook continuing to exchange views as the sides went in for the interval.
Wigan fans streamed on to the field at full-time and, although many were simply intent on celebrating with their heroes, one supporter accosted Sergio Aguero, with the City striker retaliating before being pulled away from the incident.
Objects were also thrown by some City fans in the stands as a section of the Wigan support on the field goaded their opponents, with police and stewards required to ensure the situation did not deteriorate further.
The Football Association announced on Tuesday that Aguero would face no disciplinary action, with the half-time events also not deemed worthy of censure.
Nevertheless, Mourinho was seemingly unwilling to leave the issue alone, drawing a contrast between City's downfall at Wigan and his own team being caught up in a pitch invasion at Ashton Gate when Bristol City dumped United out of the EFL Cup.
"In the Champions League we are alive. In the FA Cup we are alive.
"In the EFL Cup, after winning last season, we lost in the quarter-final but we lost like Manchester United likes to lose.
"I would say, as a Manchester United manager, that way of behaving as a big team, even in defeat we were a big team."
Wigan and City have been charged with failing to control their player in the aftermath of Delph's dismissal, while both clubs have been asked to pass on their observations on the crowd trouble after the match to the FA by the start of next week.
It is not the first time this season Mourinho has cast himself as being above City's behaviour around matches.
An incident in the tunnel after City won December's derby at Old Trafford 2-1 was reportedly sparked by Mourinho heading to the away dressing room to voice his objections over the volume of the celebrations.
Reacting to the fallout from the alleged fracas, over which the FA also elected to take no formal action, Mourinho said: "The only thing I can say is it was just a question of diversity; diversity in behaviours, diversity in education."