Early in the second-half at Selhurst Park, Reds defender Jarell Quansah made contact with Jean-Philippe Mateta inside the box.
Play was initially waved on and Liverpool thought they had got away with another penalty after an earlier incident with Will Hughes.
However, 106 seconds after the challenge was made, referee Madley paused the game and went over to check the VAR screen.
He reviewed the incident and awarded a penalty to Palace, which was subsequently converted by Mateta in the 57th minute.
Such a decision felt very delayed considering the time between the tackle and the review, and Minto couldn't believe what he was seeing.
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"What's happening here?" he said on talkSPORT commentary as Madley went over to the screen.
"Is the referee going to check the push from all that time ago? He's given a penalty! It was ages ago! If that's the case, they had to stop the game."
He added: "That's a huge decision, that's a big, big decision. Jurgen Klopp must be absolutely livid. The referee had made that decision in a tenth of a time it took to overrule that penalty earlier.
"He's literally had one look at it. I wouldn't have overturned that, I don't think it's clear and obvious. It's a decision I can't agree with. I agreed with the one that was overturned before, but I'm not having this one."
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Minto had previously criticised the role of VAR when Palace's earlier penalty was rescinded, with the challenge replayed 31 times.
He questioned the decision making once again for the Mateta incident, saying: "Stop the game if you knew you were checking - what if Liverpool or Palace scored in that time you were checking it?
"It would have been carnage. As soon as you check an incident and you know you need more time, get the referee to stop the game. It's the only way."