The Biancocelesti were forced to play for 74 minutes with 10 men after Antonio Candreva's red card for preventing a clear scoring opportunity.
"All the incidents went Milan's way," Petkovic told Sky Sport Italia. "They play very well and are in a good period of form, but with 11 against 10 of course they did better.
"I have to compliment my team, who tried to give their all to the very end. As everyone else complains about referees, I hope people don't forget about us...
"In my view on the opening goal there was a Stephan El Shaarawy foul on Bruno Pereirinha. As against Fiorentina, we paid the price for certain decisions. These things happen, but I think we could've played on a par with Milan if it had been 11 against 11.
"We tried to attack Milan, but from the 16th minute onwards it was a totally different game. It could've been different in the second half, but we couldn't get it back on track."