The union have launched an employment tribunal claim against the club on the players' behalf.
It emerged this week that the union had launched the action in relation to alleged failure to consult and inform over the transfer of contracts to Charles Green's newco club.
PFA Scotland have said they will withdraw the case if Green drops his claim for compensation for players who declined to transfer to the new company under Transfer of Undertakings (Protection of Employment) legislation (Tupe) and left for other clubs.
But Green has refused to back down and McCoist supported his stance while questioning the approach of PFA Scotland.
"I don't know all the facts and figures so I stand corrected if I'm wrong, but if I'm one of the players and I was against the action, I would probably be a little bit disappointed that I had possibly been put in a compromising situation, especially with our own fans," said McCoist, whose team visit Montrose in the Irn-Bru Third Division on Saturday.
"Our fans, who have been nothing short of sensational from start to finish through this whole process of us rebuilding, I think their noses might be out of joint if there are players who are taking the club to court and trying to get more money out the club.
"I just feel one or two of the players are a little upset at the potential of being put in a compromising position by their union, who possibly could have and should have informed them of this.
"It might have been our position to tell them that they were effectively taking us to court. I'm not sure that's the case, but it is a little bit of a dog's dinner."
The compensation claim will go before an initial arbitration hearing at the Scottish Football Association on January 7.
Rangers are pursuing damages from six of their former players - Steven Naismith, Steven Whittaker, Sone Aluko, Kyle Lafferty, Allan McGregor and Jamie Ness.
McCoist said: "I think the club and Charles in particular have every right to pursue financial benefits where they think we are legally entitled. I can totally understand that.
"The club have taken legal advice on it and feel the club are possibly due money and I would absolutely back that.
"We have probably lost in the region of £30million of players and the club feel they have the right to pursue that legal case.
"Players left for absolutely nothing, which they feel they were entitled to do.
"You have someone like Maurice Edu, who stayed and Tupe-d over and the club got a small fee for him.
"I think the fans are looking at someone like Maurice Edu, who they believe left in the right manner."
The players' union are also involved in individual employment cases for Aluko, Lafferty and Ness.
McCoist said: "I've read one or two newspaper articles from former players who have shown a little bit of concern that the maybe the fans wouldn't welcome them back, which I can understand.
"The players made their own decisions, they took advice and made their own decisions, and I think they have got to live by them.
"I'm not saying the decisions are right or wrong because everyone will look at things differently. But they made the decisions and I feel they have to stick by them."
McCoist admitted he could understand the concerns of players who feel they were bereft of information amid the transfer of assets to the new company when the original Rangers was consigned to liquidation.
He added: "It was my job to pass on information from the administrators, which I did 100%.
"It might not have seemed enough and I can understand that. But I was passing information that was being passed to me."
Meanwhile, McCoist denied Aberdeen winger Ryan Fraser was one of the players he has targeted as he bids to persuade players to join Rangers when their transfer embargo ends on September 1 next year.
McCoist said: "There's nothing in that at all. (Aberdeen manager) Craig Brown hit the nail on the head when he said he'd expect me to pick the phone up and phone him if there was any interest from Rangers.
"If we had any interest - or if we do have any interest - then Craig Brown will be the first person I call."
McCoist expects a tough contest on the artificial surface at Links Park, which is further up the north-east coast than Arbroath, where Celtic won 1-0 on Wednesday.
McCoist said: "We saw in midweek how tough it is for teams going to supposedly wee venues so it will be another tough game.
"They have been going well so they will fancy their chances being a home game.
"The surface will be a bit alien to us but we have won at East Stirling and Clyde on similar surfaces so hopefully we can handle that."