Sir Alex Ferguson's gripe about the inconsistencies in the FA's disciplinary structure was one of a series of reasons for the surprise resignation of chief executive Ian Watmore.

Other bones of contention included a Saracens rugby match being played too close to the FA Cup Final, as well as the leaking of an email about a senior appointment. None of the issues on their own caused Watmore's resignation, but he had grown frustrated with the way such matters were approached.

After the FA's board meeting on Tuesday, Soccernet was informed that it was an "accumulation" of "three or four" issues that prompted the resignation.

Ferguson was unhappy that Rio Ferdinand received an extended four-match ban after a 'frivolous' appeal earlier this year. Ferdinand had lashed out at Hull's Craig Fagan, but Ferguson felt there was inconsistency as Liverpool's Javier Mascherano escaped punishment for a similar action against Leeds in September.

"The concern is the word frivolous," Ferguson said. "The two most experienced referees in the Premier League are Alan Wiley and Steve Bennett.

"They are under the same controls and the same directions. One says yes (Bennett), in the case of Rio, and one says no (Wiley), in the case of Javier Mascherano against Leeds United when he punched the player in the back of the head. When you see that example, we don't think our appeal was frivolous."

Ferguson recently hit out again after Liverpool's Steven Gerrard was not punished having appeared to throw an arm at Portsmouth's Michael Brown.

"I didn't expect them to charge Gerrard simply because it's a dysfunctional unit, the FA," Ferguson said. "I don't think they know what they are doing.

"There's no consistency for a start. I never expect any. They'll do what they want down there. It's crazy at times."

These public complaints have drawn attention to the disciplinary system and it will now be down to the latest new chief executive to address the issues.

Chief operating officer Alex Horne has been appointed as Watmore's replacement on a temporary basis, and the process of finding a permanent candidate has now begun.

The FA insists that, although Watmore felt his position had been undermined, the professional lobby, the Premier League and the Football League had done nothing to support that claim.

Relations have been tense between FA and Premier League in the past, and that has led to political bloodletting, but the FA insists that this is not the present scenario.

An FA insider told Soccernet: "The situation is not personality-led. The board meeting was very calm, no raving, no one storming out, and no one believes that the professional game was blocking things he wanted implemented.

"Of course there have been skirmishes in the past, but there is no crisis, no war zone, no massive row between the FA and the Premier League - which might disappoint a few people, but that's the truth."

The FA's statement made it clear that the animosity between previously warring factors does not exist at present despite so much media hype to the contrary.

It read: "The board strongly believe that the FA and all of English football's stakeholders are strong and capable enough of changing and developing the game under their own authority. The board will always try to act in ways that are right for the game.

"Further to reports following Ian Watmore's announcement, the board are clear that the Professional Game has not blocked proposals for change. Additionally, the board does not accept that Ian's departure is down to any one individual or any personality clash with Ian.

"We have a very important period ahead and it is imperative we focus fully on the challenges we face, particularly as we approach the final preparations for the World Cup in South Africa and the latter stages of the World Cup bidding process. Success in these endeavours is the first priority.

"The FA is stable, working normally and as an organisation we are geared up for success."