Villa were held to a goalless draw in their Premier League visit to Selhurst Park but Emery felt that when Youri Tielemans was pulled down during a late corner, the incident should have been checked.
Earlier in the half Palace saw a penalty claim referred to VAR and the game ended with Emery exchanging words with Madley before stalking off the pitch.
“They must check the action of Youri Tielemans – it’s a potential penalty. If they check it, it’s a possible penalty,” he said.
“Brennan Johnson for me it was clear it was not a penalty, but OK they can check it.
“But the Tielemans penalty in the corner when the ball is coming and the defender was clutching him one second, two seconds, three seconds…”
Villa goalkeeper Emiliano Martinez suffered a calf injury, forcing Marco Bizot to play the entire second half and the Dutchman made several important interventions when Palace were at their most threatening.
“It’s a small injury. I’m not a doctor but he’s hurt his calf. He played fantastic in the first half and in the second half Marco was fantastic,” Emery added.
“Now we will check Emiliano Martinez with the doctor and hopefully in a few days or a week he will come back and be able to play.”
The draw means Villa were unable to capitalise on Manchester City’s 1-1 stalemate with Brighton, keeping them in third place with Arsenal’s lead at the top slashed only by one point.
“To get a point here is fantastic. We could have won more than we lost,” Emery said.
“We controlled the first half very good. We didn’t concede and we were dominating. We weren’t creating big chances but one clear one for Ollie Watkins to score.
“We lost 15 or 20 minutes in the second half because they were pushing and had one or two good chances. But we finished dominating and creating chances. We were close to winning.”
Palace boss Oliver Glasner was delighted with the determination shown by his team, who entered the clash having lost four of their last five games.
“I’m very proud and huge credit must go to the players because they were playing the most in-form team in the Premier League,” Glasner said.
“Everybody could see that in the first half we were not full of confidence and then in the second half we really got back into the game and had opportunities to win.
“Villa also created chances and the game could have gone either way, that’s why I feel the draw is a fair result. The resilience and commitment we showed makes me very proud.”