The Mexican player made a shock move from Chivas to Manchester United in 2010 and quickly established himself as a fan favourite under Sir Alex Ferguson. However, when Ferguson left after winning the club's 20th Premier League title in 2013, Hernandez believes the situation wasn't handled in the right way.
David Moyes was appointed in July 2013, and Hernandez played under him for the 2013-14 season, before moving on loan to Real Madrid for 2014-15.
And Hernandez, 31, hinted that as good as Real Madrid was when he joined them, he could've stayed in Manchester for longer under different circumstances.
"Real Madrid was a dream come true, [but] I'll be honest, I'll always be a Red," Hernandez said on Saturday during an interview with Rio Ferdinand's The Locker Room. "We never had anything personal, Moyes and myself, but it was a mistake that they took him -- and that was the first mistake that is still haunting [the club], not because of him, it's not him."
"They thought they were going to take the replacement of the boss Sir Alex so [quickly]?" Hernandez continued. "It's impossible. Even [Pep] Guardiola and [Jurgen] Klopp and [Jose] Mourinho are not at the level of Sir Alex yet, they on their way to try to get there, or [Johan] Cruyff.
Hernandez said Manchester United "definitely" got rid of the players too quickly after the Ferguson era came to an end, pointing out the club had just won the title and was a winning side.
"Aside from whether [Moyes] is a good or bad coach, his ideas, I'm not going to question that; the problem is that I don't understand really about this adaptability. How it is possible that you are not -- it's not humble -- clever enough to maintain at least half of the guys from the way it was succeeding because [Ferguson] is the greatest of all time?" Hernandez said.
Hernandez added that he became frustrated under Moyes because the club didn't accept offers for him in the summer of 2013 and again the following winter, while the striker only started six Premier Leagues games over the 2013-14 season.
"[Moyes] lasted the seven months he lasted because he was so stubborn," stated the Guadalajara native. "He didn't have adaptability and that growth or acceptance. You need to grow to be at United."
Mexico's all-time top scorer eventually went to speak to Ferguson to discuss the loan move to Real Madrid, with the former manager advising him that playing for Los Merengues was a difficult opportunity to turn down.
In the same interview, Hernandez added that Michael Carrick was "one of the most underrated players in history" and praised Ferguson for his man management skills.