The Germany international believes that Pep Guardiola's men were punished for their carelessness and complacency as the Premier League side won 3-2 at the Allianz Arena
The reigning European champions appeared to be on their way to a comfortable victory early on as Muller and Mario Gotze gifted Pep Guardiola's men a two-goal lead but the Premier League side turned the game on its head with goals from David Silva, Aleksandr Kolarov and James Milner.
"I think we showed our human side against City," the Bayern forward told Uefa's official website.
"We were too careless at times. It was not as if we gave away chance after chance but we did not look good on any of the goals we conceded.
"It is no secret that City are always good for a goal but we got off to a great start and put them under a lot of pressure. After that, we took our foot off the pedal.
"We need to get that winning mentality into our heads. Maybe it is understandable that we got a bit complacent after so many wins but we are professionals, so that kind of thing is not acceptable."
Despite the defeat, Bayern pipped City to top spot in Group D due to their better head-to-head record, having beaten the English club 3-1 at the Etihad Stadium on matchday two.