Kwabena Appiah, Vitor Saba, Daniel Mullen and Seyi Adeleke all left the club last month but, before their exits, were reportedly ostracised from the rest of the team by Popovic and made to train on their own.
Relations between the Professional Footballers' Australia (PFA) and the Wanderers are already tense with the union strongly criticising the club over the payments made to players for reaching December's FIFA World Club Challenge in Morocco.
With that issue still to be settled, the Asian coach of the year said he was unconcerned by claims his treatment of the four players was in breach of the code's Collective Bargaining Agreement.
"I have nothing to answer there. We're very happy with the how we operate as a football club," Popovic said.
"I can't speak for how other clubs operate but I'm very proud of the way we work, day in day out."
Mullen will face his old club in a Newcastle shirt on Saturday at Hunter Stadium in the battle of the A-League's bottom two sides.
The Wanderers - winning their first game of the season at Penrith last week, with a 2-0 defeat of Wellington - will move off the foot of the table with a win over a crisis-hit Jets side.
When the two teams last met at Pirtek Stadium in November, they played out a 1-1 draw, but eight of the side who played for the Jets in that game have since been shown the door by owner Nathan Tinkler.
Coach Phil Stubbins saw his side battle bravely against Brisbane last Friday only to concede a 93rd-minute own-goal from Allan Welsh that consigned them to a 2-1 defeat.
But despite the dramas surrounding Saturday's opponents over the past month, Popovic is still expecting a tough game.
"Both teams are desperate for points and we won't take them lightly," Popovic said.
"We always feel we can beat anyone and this is no different. But we're still bottom and behind Newcastle and we have the chance to go above them with a win tomorrow.
"Anything less that the commitment and effort we put in last week won't be enough.
"For us, it's about improving on last week's performance."