The Rossoneri lost 1-0 despite Yuto Nagatomo's red card after 48 minutes, but they were furious at several controversial decisions.
"Seeing as I never talk about referees, I'm afraid I have to now. The referee affected the game," snapped Allegri on Sky Sport Italia.
"It was a technical error, as he blew the whistle for half-time 12 seconds early. There was a last man foul on Emanuelson which was given against him. There was maybe a penalty on Robinho, the Nagatomo red card was obvious as he couldn't not give him another yellow for that.
"This is not an alibi and perhaps today the referee was unlucky, but the incidents were really obvious.
"I have no idea what the referee whistled for on the Montolivo goal. Let's just say he was unlucky on the decisive incidents, as the goal would've been crucial, there was a penalty and Samuel was last man too.
"It's not as if the referee did us a favour with Nagatomo's red card, as he obviously stuck his arm out for an intentional handling offence.
"It's a shame we are running into some decisions that go against us, but we can't do anything about that. Maybe the referees are on as bad form as we are."