It was a game of controversies as the Black and Gold were forced to finish the game with nine men on Wednesday.
Ghana defender Jonathan Mensah was the first to take an early shower following a 35th minute red card for bringing down C.J Sapong.
"I take issue with everything, the whole performance with these referees," Berhalter said, as reported by his club's official website.
"The first thing is, no matter how you look at the Mensah challenge, he ends up winning the ball trying to play the ball. He gets thrown out and it's a penalty kick.
"I'm not even sure it's inside the penalty box. When any type of contact is initiated, he comes away with the ball."
Compatriot Lalas Abubakar was the next to face the wrath of referee Ismail Elfath, picking up a second yellow card 14 minutes to full-time.
"Lalas gets hammered as the ball is up in the air," Berhalter continued.
"The referee calls a foul. Ilsinho is trying to block Lalas from getting the ball and playing on. He does a swim type of move to get around him and he gets a red card.
"Ilsinho should be ashamed of himself. That has no place in soccer, that type of acting. No place. He's really hurt? He got hit in the face? Seriously?
"Again, to me the whole presentation of the game was disgraceful.
"These referees, the way they officiated this game has nothing to do with soccer."
Crew currently sit sixth on the league table.