Celtic also expressed concerns about offside decisions given against recent loan signing Robbie Keane.
SFA president George Peat confirmed that there has been a private meeting between the ruling body and Celtic on the issue but hit back by questioning the courage of the Parkhead source and the timing of the leak.
The furore has served to intensify the scrutiny that will be on Sunday's referee Dougie McDonald as the visitors seek to reduce the seven-point gap behind SPL leaders Rangers.
However, Boyd believes Celtic were correct in approaching the SFA - and letting it be known through the media.
"I would imagine Alex Ferguson would be proud of the timing of this," he told BBC Scotland.
"Certainly on the evidence of what we have seen so far in this campaign, there has been some outrageous decisions and Celtic have a bigger grievance than most.
"So it was not before time, it was something that should have been looked in to.
"Is there ever a right time for anything like this to come out? I suppose not but it had to come out at some stage.
"It has come out at this time and Celtic are doing the right thing, expressing their concerns.
"There is certainly not (bias against Celtic), just a lot of incompetence and it has probably been highlighted by Celtic in their approach to the SFA."
Boyd, who played for Celtic between 1992 and 2003, continued: "You have to look at managers who have echoed some of the sentiments that Celtic fans have been feeling.
"Craig Levein, when he was manager at Dundee United, was disappointed that his defender Darren Dods didn't hold on to the ball with both hands when he should have given a penalty away (at Celtic).
"Eddie May, when he was Falkirk manager, said Celtic should have had a stonewall penalty.
"It's not just penalty decisions, other decisions have been mystifying.
"Incidents like Lafferty's challenge on Hinkel in the last Old Firm game which was just a yellow and everyone saw that it should have been a straight red.
"So Celtic are doing the right thing, expressing their concerns."
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