The Red Devils chief has admitted that he had to deal with several disappointed players in his camp when he named his team ahead of Wednesday's 1-1 Champions League last-16, first-leg draw at the Bernabeu.
Mexico international Hernandez was one player left frustrated at being an unused substitute, with Danny Welbeck favoured to play along with Robin van Persie and Wayne Rooney, who dropped deep throughout.
Welbeck's inclusion raised the most eyebrows given that he has struggled in front of goal this season. But Ferguson got that decision right as the England international's header handed them a vital away goal.
On Hernandez's absence, the Scot said: "I explained to Chicharito that Robin van Persie is our main striker and we wanted someone to join in from a deeper position.
"Whenever Chicharito plays, he delivers. He has 14 goals, he will score more than 20 and will have opportunities."
Meanwhile, Ferguson also revealed that Ashley Young and Nani were also put out at not being considered to play in the massive match.
He added in the Daily Express: "There were a lot of disappointed players.
"Nani and Ashley Young - international footballers - I found it hard to explain to them I was leaving them out."