Jean-Philippe Mateta joined Crystal Palace in 2021
Mateta was on the verge of joining Milan for £30m on deadline day, but the deal was called off after knee issues emerged over the course of two medical examinations.
The 28-year-old has been dealing with the injury to his right knee during the first half of the season.
"We knew and he knew there was an issue. He was not really pleased," Glasner said.
"We took a higher risk, that's why he could play in most games, but we rested him for some games and some training sessions.
"To be honest it was not a big surprise to everyone that he could fail [the medical]. We knew that this can happen and he knew it."
France international Mateta has yet to decide what his next steps should be, with this summer's World Cup on his mind.
"There are two ways we can do this: manage the knee like we have until after the World Cup, which is Mateta's dream to play in. The other one is he undergoes surgery," Glasner said.
"We don't know how long he would be out. There are a few predictions: it could be two months, three months, six to nine months. There are many opinions, but it is about doing the right thing and we will decide next week."
Mateta ruptured his meniscus in 2019 when playing for Mainz and spent about six months on the sidelines following surgery. A similar absence this time would end his World Cup hopes, with the tournament just four months away.
Dwight McNeil has scored 15 goals and provided 19 assists in 120 appearances for Everton
Despite retaining Mateta, who is Palace's top scorer with eight league goals this season, the Eagles paid a club record fee to sign striker Jorgen Strand Larsen from Wolves.
Palace were also on the verge of bringing in Everton winger Dwight McNeil until the deal fell through late on deadline day.
Glasner said he had "learned to accept situations" after Palace were also unsuccessful in finding a replacement for captain and centre-back Marc Guehi, who joined Manchester City earlier in the window.
"At the end of it, the club tried everything with huge offers and huge bids for a Marc Guehi replacement, but clubs said they don't sell on deadline day," Glasner said.
"Credit to the club that without getting any money for Mateta they still spent a big fee on Strand Larsen.
"On the other side, McNeil was the last one we thought we could finalise, but in the last minutes the terms of the deal changed again and the deal failed. I expected him and planned for him in the next day's training."
McNeil's partner, Megan Sharpley, criticised Crystal Palace on social media for the way they handled the situation.
"He's in and he's training as well, so Dwight's OK," Moyes said.
"We understand exactly where it went wrong, how it broke down. He knows everything about it and there's no problems there.
"We had given permission for Dwight to go and have a medical and do all of the things required for it, so it was very hard to do much more than we have done."
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