The Premier League voted on Monday to start training with immediate effect in an attempt to resume the English football season.
Many players including Danny Rose, Troy Deeney and Chelsea’s Tammy Abraham have raised concerns over the possible return of football, with the Watford captain saying he will not return to training this week amid concerns for his own son's health.
Neville, who was speaking on The Football Show on Sky Sports, said many players are uncomfortable with the return of football and believes there will be a lot of problems over the coming weeks due to the threat of Covid-19.
"I know there are Premier League clubs with five or six players who don't want to return or are uncomfortable with certain things around stage two or three," the former Valencia head coach said.
"We do have more problems and issues to resolve over the coming weeks."
Despite a lot of concerns about the resumption of the Premier League, former Liverpool defender Jamie Carragher said on the same show that he believes the league will be back this summer.
He said: "We have always said on this show that if a player does not feel safe or sound to go back, he can't go back.”
“This was always going to be the case that maybe one or two players in every squad may not feel safe and may not want to go back.”
"I do not think that would stop the Premier League going on. If players en masse said they did not want to be involved, then that would be a big problem.”
"But if one or two players in every club, that is something the clubs and Premier League will just have to accept and try and get them on board going forward."
Carragher added: "The Bundesliga has returned and I'm very confident that the Premier League will restart. This is just the start.”
"A player will test positive for Covid-19 today and there will be more questions to get through in the different phases but I am a lot more confident than l was a month ago that the Premier League will start.”