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Stajcic's side had twice taken the lead in Friday's A-League clash, only for the Reds to be awarded a spot-kick each time, with both being coolly converted by Tomi Juric.
The Socceroos striker then stepped up after United were awarded a third penalty in the 83rd minute and dispatched it to complete his hat-trick of spot-kicks, ensuring the Reds stole all three points.
The Mariners were clearly the better side for much of the night and deserved more from the clash which was marred by VAR and the penalty decisions.
"Of course, it's affected the result," Stajcic said.