The SFA has been involved in several controversial decisions this season.
Craig Gordon was critical after Celtic defender Kristoffer Ajer was kicked out at by Rangers goalkeeper Allan McGregor during the Old Firm derby.
McGregor faced no punishment for his actions.
Gordon said of the process: "It seems quite a clouded subject on how they get to these decisions."
He added: "As far as I'm aware, it goes to three referees. There's no comeback and you don't know who they are. It's a strange system.
"You never know who the referees are, who their allegiances might be."
The SFA recently wrote to FIFA asking for clarification over what constitutes a red card offence.
"I think everybody was surprised by the decision," Gordon said of the incident with fellow Scotland goalkeeper McGregor. "I don't think anybody thought that would be the outcome.
"We just need to know exactly what's happening, what is violent conduct, what's not and then everybody abides by those laws and we get on with it.
"It's happened now, that's the decision. We move on. It's no big deal."