The former Scotland international was speaking after a range of controversial decisions were made by the SFA's disciplinary committee in recent weeks.
One of the most controversial of which was in the Old Firm derby, when Gordon's opposite number Allan McGregor was not penalised retrospectively for appearing to kick Kristoffer Ajer.
Speaking about the appeals process, Gordon said that "It seems quite a clouded subject on how they get to these decisions.
"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."
Gordon admitted that he was surprised at the lack of action taken against his former international team-mate McGregor, but accepted that everyone had to accept the decision and move on.