The Manchester City captain was dismissed by Mike Dean at Arsenal on Sunday for what he deemed to be a dangerous tackle.
Although the incident itself was borderline, most observers believed the FA would stand behind Dean and leave Kompany to serve a three-match ban, but the disciplinary panel had other ideas and cleared the City player.
While Ferguson is wary of adding to the debate, believing his comments will be deemed biased, the Scot does feel the FA have not done themselves any favours by failing to back match officials over incidents that do not appear to be clear-cut.
"Anything I say in that situation will be regarded as biased, so I am not going to bother with it," he said.
"But it is very unusual.
"It does open the door of course, but that is their (the FA's) problem."