Football Australia's (FA) referee department concedes Shaun Evans got it wrong in the two controversial decisions that cost the Central Coast Mariners in their A-League Men match against Melbourne City.

Refereeing and the VAR came under the spotlight again after the Mariners were denied what appeared to be a clear penalty in the 87th minute of their 3-2 loss.

The Mariners were trailing City when Mathew Leckie stepped on Lewis Miller's foot.

That followed Melbourne City's first-half equaliser coming via a contentious penalty call against Kye Rowles, who appeared to initially foul Marco Tilio outside the box, but was ruled to have done so in the area.

On both occasions, referee Evans consulted with VAR Kris Griffiths-Jones, spending several minutes reviewing footage before upholding his original decisions.

In a statement on Wednesday, FA said after a review of both decisions Evans had made the wrong decisions on both calls.

FA said City's penalty should not have been awarded due to the secondary contact in the area being "negligible".

It also ruled Leckie had fouled Miller and a penalty should have been awarded to the Mariners.

The statement did not disclose whether Evans would be stood down.

After the match, Mariners coach Nick Montgomery said the decisions had cost his team dearly and had set the A-League Men competition back.

"It's tough for referees to make calls, the game is so quick," Montgomery said.

"But when you have VAR, and I'm looking at the screen and I can see [the Miller incident is] a penalty, and I can see that the first one is outside the box, maybe they need to get together and really have a look at it.

"There are a lot of positives here. It's been a transition with everything that's gone on, but nights like tonight really set the competition back and it's sad for football."

Miller — on the bench after Leckie's challenge left him with a gash on his foot — could be seen saying, "What is the point of VAR?" on the TV coverage when Evans upheld the late decision.

Montgomery stressed VAR decisions needed to be made quickly to get the game moving again.

"Everyone watches the (English) Premier League. Why do we watch the Premier League? Because it's the best league in the world," he said.

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"It's fast, frenetic, it's physical, it's quick and that's why everyone watches it.

City star Jamie Maclaren scored from the earlier controversial penalty but lamented the preceding delay.

"In the first half when I had the penalty, when it drags on and drags on, you start questioning where you're going to put it," Maclaren told broadcaster Paramount+.

"He's got a tough decision to make, but you want them quicker.

"Because players, we ended up having a conversation with the Mariners boys for about three or four minutes which you don't normally do and [it] shouldn't happen.

"So we want it quicker and also consistently."

AAP/ABC