Australia's top football referees believe Phoenix defender Ryan Lowry should not have been sent off against Perth Glory on Sunday.
But the club's appeal to have his red card rescinded has been rejected.
Lowry was sent off by Adam Kersey after the VAR reviewed a tackle where his studs brushed a Glory player's legs following a tackle.
Referring to the incident, Football Federation Australia referees' director Ben Wilson said that in a post-round review involving himself and the FFA's senior referee coaches, "the correct outcome should have been a yellow card for a reckless tackle".
But the Phoenix appeal to the separate Match Review Panel was dismissed because the panel "can only overturn a red card if all three members determine no card was warranted".
Wellington Phoenix chairman Rob Morrison called for the FFA to be held accountable for the decision.
Morrison told Radio Sport's Jason Pine it was not simply a case of censuring the referee involved.
"We've had issues with the VAR last season and this season, and I think we have to look higher up the food chain.
"The referees have bosses, the referees' assessor has a boss. Those are the guys who should be held accountable for this and it is impacting the game," Morrison said.
"What you demand from them is consistency and clarity, and we don't get that from the refereeing. There needs to accountability and the FFA needs to be held accountable for this and they are not."
Morrison said the Phoenix often have Kersey in charge of their games.
"We get inexperienced referees. I think there is a clear bias against the Phoenix. The referee [against Perth on Sunday], he goes out, tries to do a job, he doesn't pick which games he gets, but he's reffed 21 games in four or five years in the A-League. Eight of those games have included the Phoenix. That's not a statistical anomaly, it's a statistical bias."
Morrison said at some point, the FFA have to look at the assignments and "fairly allocate the referees".
"We don't get the experienced referees and it impacts our games."
Morrison also said an issue was the lack of funding going into refereeing.
"The clubs have all demanded that the FFA needs to invest more money into referees. We have some full-time referees now but you've got to do the same with the assistant referees."
"Frankly, I don't know why they're called assistant referees because they don't assist the ref. They are linesmen or linespeople, and we should go back to calling them that until such time as they start making decisions."