Ferguson's comments about Webb being the "best man for the job" were largely innocuous but an FA statement said they had contravened rules about commenting on referees in the build-up to matches.
News of fresh disciplinary proceedings against Ferguson comes as United are poised to clinch a record 19th title against Blackburn Rovers on Saturday.
In comments to the media ahead of last Sunday's game with Chelsea, won 2-1 by United, Ferguson had welcomed the appointment of Webb for the match, while stating he hoped his team enjoyed "a little bit of luck" from officials.
"He's definitely the best referee in the country, there's no doubt about that," Ferguson said of Webb, who refereed last year's World Cup final between Spain and Holland.
"We are getting the best referee and we hope it's our turn for a little bit of luck," Ferguson added.
Short link: