Manager Steve Clarke has been charged for saying Steven McLean should no longer referee Kilmarnock matches because he cannot handle "the burden" of overseeing his father's former club.
Three Kilmarnock players were sent off in Aberdeen's 1-0 Scottish Premiership win on Saturday, with one rescinded.
Clarke described it was the "worst refereeing performance I've ever seen".
The Rugby Park club have said he will face a 9 May hearing for indicating "bias or incompetence" by an official.
Kilmarnock will respond further to the charge in due course.
Clarke was given a suspended two-game ban in October for claiming an appeal over a sending off was rejected because the official in question had been appointed to referee the impending Old Firm game.
The Rugby Park manager was charged with "failing to act in the best interests of football" after a six-hour hearing. The sanction would have been wiped had there been no further breaches this season.
McLean's father Stuart played as a full-back for Kilmarnock from 1974-1990, making more than 500 appearances.