The Steelmen have loaned Adam Cummins to Dundee and were looking to loan another player to the Championship side in order to finance the signing of Henri Anier, himself on loan from Viking Stavanger.
However, the new Scottish Professional Football League set-up only permits clubs to recruit one loan player from any other team.
Dunfermline signed Jordan Moore, Ryan Ferguson and Luke Johnstone from Dundee United last summer, although they will escape punishment as they were working under the auspices of the Scottish Football League before the amalgamation with the Scottish Premier League, which brought with it a new SPFL rule book.
Ahead of the Scottish Premiership clash with Hearts at Tynecastle on Saturday, McCall said: "We have needed to get players out to finance the Anier deal.
"Adam Cummins has gone to Dundee and there was an opportunity for another of our players to go there also.
"It looked like that was going through and this new rule has come up.
"We didn't know, Dundee didn't know, I don't think many clubs knew.
"Since the rule book amalgamated, only one player from each club can go to another club.
"I am flabbergasted.
"It is more frustrating for us because we have been trying to do this deal which would help finance Henri.
"We will no longer be able to get the finance from Dundee which were hoping to get from one of our players.
"It is nonsensical. There is no reason why two players can't go from one division to another division. I think the rule is crazy.
"I can understand not three or four but one only? And why should cross-border be different?
"St Mirren have got two players from Newcastle. That is not a dig at them.
"They are working under FIFA rules and we are working under Scottish rules.
"Dundee United have loaned three player to Dunfermline and it has now come out that they have gone against the rule book but they are not guilty of anything, really.
"It was apparently flagged up earlier so surely someone should have notified all the clubs.
"I spoke to Neil Doncaster (SPFL chief executive) at length this morning and he totally agrees with me.
"I think they have a meeting on Monday and that will be brought up."
McCall remains confident that the finance will be found from somewhere to sign Anier.
The 23-year-old Estonia international has been on loan at Fir Park since the summer.
The former Bradford boss said: "There has been a lot of stumbling blocks.
"I think we are almost there but there is no confirmation as yet.
"We are looking to keep him as our player, to take over his contract and add a couple of years on. He is available to play tomorrow.
"If it doesn't happen this afternoon, we are hoping it will be concluded over the weekend and he will be a Motherwell player."
Meanwhile, Jack Leitch has been added to the Motherwell squad for the Scottish Premiership game against Hearts at Tynecastle on Saturday.
The 18-year-old midfielder comes in for Adam Cummins who has gone to Dundee on loan.
Defender Fraser Kerr (hamstring), goalkeeper Lee Hollis (ankle) and forward Lee Erwin (knee) remain out.
Provisional squad: Nielsen, Ramsden, Francis-Angol, McManus, Hutchinson, Hammell, Ainsworth, Lasley, Vigurs, Carswell, Lawson, McFadden, McHugh, Anier, Sutton, Moore, Stewart, Leitch.