At one stage, Benitez seemed close to getting the sack when a dispute erupted with American owners George Gillett and Tom Hicks over moves to sign new players during the January transfer window.
Liverpool were struggling and their Champions League campaign was on the brink of a financial crippling group stage termination.
Since then, Benitez's team have stabilised the situation, advancing to the last 16 of Europe with a four-goal hammering of Marseille on Tuesday.
The situation hardly warrants talk of a crisis and given Benitez has won a European Cup - and taken Liverpool to another final - as well as an FA Cup, Ferguson cannot comprehend why the Spaniard has been under attack.
"I can never understand where criticism comes from," he said.
"Rafa has a great record but all of a sudden you read about a supposed dispute between Rafael Benitez and his directors.
"Other people take more of an interest in Liverpool than me but there is obviously some undercurrent of a dispute running somewhere along the line, which is strange considering his record."
"Rafa won the European Cup after being 3-0 down to AC Milan, which is an amazing feat," continued Ferguson.
"And there was no disgrace in losing to AC Milan last season.
"I don't know where criticism starts or how it starts in our game.
"But with Rafa's record, it will be disappointing for him."