The Premier League champions were denied a penalty in the dying seconds of the match as well as seeing a Sergio Aguero strike disallowed having fought back from a two-goal deficit.
Afterwards, Mancini raced onto the field and confronted referee Peter Rasmussen before criticising him in front of reporters.
When asked what he said to the referee, Mancini responded: "I said it was a goal. I didn't see the last situation with Mario that was a penalty. I said it was a goal.
"The referee and his staff were really poor tonight."
Mancini could now face a touchline ban which would see him miss his side's crucial home match with Real Madrid.