Roberto Firmino and Mohamed Salah are two of the Liverpool players who were affected by this decision
Premier League managers backed the decision of clubs not to release players from red-list countries during September’s international break.
Current UK government rules would force players to miss multiple games due to the 10-day isolation period upon return.
Pep Guardiola, Manchester City's boss, said that it was "nonsense" to let players go.
"We pay players to play three games, then play Leicester [in Premier League]"
He said, "They are isolated without any training for one week or 10 days so it makes no sense."
"We must say again today what the position is of the club, and the Premier League. It is not just Manchester City. It's a problem with the calendar and the schedule.
The Premier League and Football Association met with the government to discuss the possibility of players being exempted. However, they failed to reach a solution. As a result, clubs decided not to release players "reluctantly, but unanimously".
Jurgen Klopp, Liverpool manager, says that the possibility of a 10 day quarantine for his players upon their return to Liverpool would pose a risk to their health.
He said, "When players are on international duty, it's not great for club managers but it's still done, we never moan." "In this instance, it's different because England has different rules.
"If you are returning from a country on the red-list, you must quarantine for 10 nights in a hotel. You cannot choose a hotel, or a hotel chosen by someone else, near the airport. It's far from a spa hotel. It's waiting, eating, and sleeping.
"We cannot do that as a club, not only because they lose them for games, but also because we lose them during 10 days of training. Ask any doctor or sports scientist and they will tell you that muscle can be lost without moving it. It's risky to start training again, and you may lose your muscle.
Dean Smith, Aston Villa's boss, said that it was difficult for organizers but that he didn't think footballers should be exempted from current rules.
He said, "This pandemic has placed us in a situation where they'd need to quarantine at a government hotel then detrain."
"The World Cup qualifiers must be played at one time. Although it is difficult, I believe you cannot make exceptions for footballers. It's way beyond my pay grade."
Patrick Vieira, Crystal Palace's boss, said: "I think all managers and all clubs are waiting for the decision. If a country is in the red zone, it will be difficult to allow our players on international duty.
Premier League chiefs were also dissatisfied with Fifa's decision in October to extend the September and Oktober international windows by two more days in South America. This was to allow countries to catch up on World Cup qualifying matches that had been delayed due to the coronavirus pandemic.
This means that matches can be played on Thursday 9 September and Thursday 14 October. Players involved will be released for 11 days.
Due to the time difference, players who were involved in these games may not be able to return to their clubs until Saturday 11 September when eight Premier League matches will take place.