Croatia boss Zlatko Kranjcar was angry at the goals scored against his side but refused to comment on English referee Graham Poll after the 2-2 draw.
Croatia's Dario Simic and Australia's Brett Emerton were sent off before Josip Simunic was finally dismissed after being shown three yellow cards.
He said: "One goal was perhaps offside, the other possibly wasn't a penalty.
"We are sad but we must look to the future. I don't want to comment on the referee. We missed our chances."
Australia fought back twice to deny Croatia a place in the last 16 of the World Cup as Guus Hiddink's side finished runners-up to Brazil in Group F.
Croatia had gone ahead after just two minutes when Darijo Srna's blistering free-kick rocketed into the back of the net.
Australia got the result they wanted and that's all there is to it
Croatia boss Zlatko Kranjcar
But Craig Moore equalised with a penalty before Harry Kewell cancelled out Nico Kovac's strike.
"We didn't play the way we wanted to after an early lead," added Kranjcar, whose side leave the tournament without a win.
"My players sat back on it although I instructed them otherwise. Australia got the result they wanted and that's all there is to it.
"We missed our chance to secure a second round berth against Japan (0-0). If we had won there, a draw would have been enough for us."