Referee Chris Kavanagh awarded a spot-kick in the 54th minute against Maxence Lacroix, who earned Palace the lead in the first half, for holding attacker Matheus Cunha.
The infringement began outside of the box, but Cunha did not go down until he had reached the penalty area.
Despite Kavanagh solely awarding a penalty kick, VAR intervened and after four minutes, the referee brandished a red card for the denial of a goalscoring opportunity following a visit to the monitor.
Palace boss Glasner believes Lacroix, who will miss Thursday’s trip to Tottenham, was hard done by.
“The red card changed the game completely,” Glasner said. “A penalty and a red card is a very harsh decision because the foul started outside the box and usually the foul has to be given where it starts.
“Matheus Cunha was very smart to wait until he was inside the box before falling.
“I spoke to the fourth official. They had to check first whether it was offside or not, then whether it was a foul or not, then where it started and whether it was a red card or not.
“It’s three or four situations to judge and this takes time but it feels like it was the wrong decision so it doesn’t make it better if it takes less time. But we have to accept it.
“It’s not a penalty, maybe he could have conceded a red card with the foul outside the box. This is what can be discussed. Maybe it’s a bit of the Old Trafford bonus.”
United captain Bruno Fernandes scored the resulting penalty before Benjamin Sesko headed past Dean Henderson to claim all three points.