While many might have chuckled at Sir Alex questioning Alan Wiley's fitness, no one is laughing at the FA's headquarters and Benitez's joke at the expense of referee Phil Dowd is not to be taken lightly either.
Benitez's case comes up on Tuesday morning, and the defence will be producing the audio and video evidence of how the Liverpool manager reached for his pocket and brought out his glasses, when he was asked about the performance of Dowd after the opening day of the season defeat by Spurs.
The assembled media may have been laughing their heads off at Benitez's joke, but the FA feel it was at the referee's expense. Indeed, they will view it as being a personal attack and Benitez looks likely to be hit with a fine, and maybe even a touchline ban.
The next case on the agenda is Sir Alex and, if Benitez gets away with just a fine, then the United boss will expect a degree of consistency. However, if the FA hit Benitez with a touchline ban for his jibe, then Fergie can expect the same sort of treatment.
Ferguson has apologised, but retained his belief he should be able to question the fitness levels of officials. No-one else, though, has raised it before, at least publicly.
While Ferguson's official statement has not gone down well with the referees' union, who are out for blood, it will not be seen as more than "damage limitation" on behalf of the FA. Indeed, the FA have given him an extension to provide his written explanation as he is currently in New York, apparently property hunting.
The statement was produced with the United boss still in New York, but it will cut little ice with the FA when he returns this week to hand in his letter of explanation by Friday's extended deadline. Charges are sure to follow and it will then be at Sir Alex's discretion whether he seeks a personal hearing.