Palace won 3-0, but not before Mateta was stretchered off after an ugly collision with Millwall goalkeeper Liam Roberts, who was sent off.
Palace eventually won 3-1 through an own goal from Japhet Tanganga and efforts from Daniel Munoz and Eddie Nketiah. The Lions struck through Wes Harding.
Glasner later said of Mateta: "He is conscious and he is in hospital. His ear looks terrible. It's a very serious injury so we hope all the best for him. We are not really happy, we can't be really happy. Of course, it's a great win and into the quarter-finals but when you lose a player, especially with a foul like this, you have two different feelings in your stomach.
"Honestly, I didn't want to see it, I just watched it and it is terrible. I'm sure the goalkeeper didn't want to injure JP in this situation, no player wants this. But f you got to the ball with this with this intensity, with the foot at that height, you can't do it because it's so dangerous and we all have responsibilities for our health. I don't want to blame him but it is a terrible foul.
"I didn't see it like it was in the game, it was so quick, I could see the keeper had a lot of intensity, but he touched the ball first. But I could see it now in slow motion and it's worse."
On his players' reaction, he continued: "The players did well until 55th minute in the first half. We controlled the game and the lead was 2-0 and we gave them unnecessarily the ball before half time and then all of a sudden it's 1-2. They got back their belief. Second half wasn't the best half, didn't create a lot of chances but Eddie decided the game - an amazing header.
"Now after watching, it is tough to talk about game because I have this clip (of the challenge on Mateta) in my mind.
"Going to quarter-finals in the FA Cup , great achievement. Fingers crossed and hoping all the best for JP."
On Nketiah, Glasner said: "He needs to get back into the rhythm. You need this rhythm in the competition, in competitive games. Keep gong stay in the game, waiting as a striker. They played a deep block and he had to wait and then he decided the game for us.
On whether Palace can win the FA Cup, he concluded: "It's winning the quarter-final. Lets see, the draw is tomorrow, lets see what team we will face. At the moment we are just waiting good news for JP. Hopefully he is back then."