Referee Peter Rasmussen was thrown into the spotlight from the start, with Yaya Toure going down in the area under a challenge from ex-Liverpool man Christian Poulsen only for the protests to be waved away.
And, in the final stages of the match, Sergio Aguero had a goal disallowed despite Aleksandar Kolarov seemingly onside and Mario Balotelli fell to ground in the area after having his shirt tugged, but again no penalty was given and Mancini was left furious.
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“The referee and linesmen had a bad night. It should have been a goal [Aguero’s disallowed effort],” Mancini told Sky Sports.
“We were close to getting the miracle we needed. Unfortunately we took only one point and I think we are finished in the Champions League now.
“I think we played a good game. We did very, very well in the second half, creating a lot of chances and scoring three goals [including disallowed goal].
“But the referee and his linesmen were really poor.”
The Italian marched on to the pitch after the final whistle and confronted Rasmussen, but when asked why the goal was not counted Mancini was non-plussed.
He continued: “I don’t know [why it did not count]. I said it was a goal and not offside.
“I don't know how it is possible for one linesman to consider that wasn't a goal - incredible.”
Despite the questionable decision against City, Mancini was under no illusions that his side simply should have done better in the match, highlighting the poor defending for Siem de Jong’s double.
“We made two mistakes and can't afford to concede goals like this,” rued the Italian. “We should have paid more attention in those situations in an important game like this.
“We have two more difficult games and we still need to try and win, nothing has changed there. We will try and get into the Europa League if that is possible.”