The Blues boss was annoyed at his side’s slack defending, and the reaction of former skipper Carlos Tevez - who refused to take the field as a second-half substitute - didn’t help his post-match mood.
And all that after an opening half-hour in which the manager saw plenty of positive signs.
Mancini said: “After we conceded the first goal we should have paid more attention - we conceded a stupid goal. When they scored the second goal, the game was finished.
“We played very well for 30 minutes, when we had a chance. But at this level if you don’t run for 90 minutes you have a problem. We didn’t work very well after 30 minutes.”
With City desperate for a goal, Mancini sent on Nigel de Jong, Aleks Kolarov and James Milner with last season’s top scorer Tevez sat resolutely on the bench.
The boss said: “He refused to come on the pitch. For me that is a bad situation. It’s impossible for a player to refuse to help the team. I can’t accept that one player refused to go in.”
Tevez later told Sky: “I wasn’t feeling good, physically or mentally.”
Edin Dzeko was not happy to make way for De Jong either. Mancini said: “Edin was disappointed but the manager must do what he thinks best. One player can’t play very well every game and I thought it was better (to substitute him). I have to speak to him later.”
City now have just one point from their opening two Champions League games with a crucial double header against Villarreal up next
Mancini said: “Tonight we had a problem in this game. Before, we haven’t had a problem.
“Maybe at the moment this team (Bayern Munich) is too strong for us, but we have a chance to go through, we still have four games to go and all is not lost.
“Maybe we can win the second game when they come to Manchester. Maybe we can beat them then.”
Centre-half Kolo Toure, who saw centre-forward Mario Gomez score both goals, said: “We didn’t defend as we have been doing, and in the Champions League you have to defend well from start to finish.
“Bayern are very experienced, they’ve been in the Champions League a long time. All we can do now is try to learn from this defeat.”