Philippe Coutinho had given Liverpool a 24th-minute lead at the Etihad Stadium before Vincent Kompany and Alvaro Negredo scored to maintain City's 100 per cent home record.
However, prior to Coutinho's goal, Liverpool winger Raheem Sterling was incorrectly flagged offside when one on one with Joe Hart, and the visitors had two penalty appeals in the second half for challenges on Luis Suarez by Joleon Lescott.
Rodgers queried why Bolton official Mason was handed the game between the title rivals and was upset at the overall standard of officiating.
When asked about the incidents, Rodgers said: "Where do you want me to start?
"I thought we never got any decision. The linesman on the offside one - he wasn't even on the same cut of grass.
"If you're working at this level you have to get it right. It's not even a difficult one.
"It is a perfectly-timed run and he is given offside when he is through one on one on goal. These are big moments in big games.
"There is another incident when Luis (Suarez) doesn't get a free-kick when Joleon Lescott went right through him.
"It is arguable it is a penalty at the end. Luis Suarez can't jump because he is tugging at his shirt.
"I thought it was throughout the evening. Hopefully we don't have another Greater Manchester referee again on a Liverpool-Manchester game."
Rodgers added: "I was very proud of the players. I thought they were outstanding and they had no help from the officials.
"I don't want it to cloud the performance of my team. I never speak about officials, I normally stay clear of that, but I feel I need to protect the players.
"The officials make mistakes, I just felt the mistakes made tonight shouldn't have happened at this level. This is a big game."
In terms of his side's performance Rodgers felt they acquitted themselves well against a team favourites for the title.
"The level of our game was high, we had chances and we didn't take them," he said. "They were outstanding and really took the game to a top side full of top European players.
"We are disappointed not to have won the game, never mind losing the game.
"We showed great confidence and belief, scored a wonderful goal and could have had a few more but there are things to learn from the goals we conceded.
"I was here at the Bayern Munich game when they were outstanding (beating City 3-1) and apart from that every other team City have played here they have scored a hatful of goals.
"I think people go away and look at us as a team that is hopefully going to be up there challenging.
"Our main intention is to set up camp in the top four. That is what the club has been striving for for a number of years.
"We have shown this year we are hopefully going to be up there and doing that. Performances like tonight and Tottenham (a 5-0 win) show we have the quality to do that."