Lending his voice to the criticism was the top US diplomat in Havana, James Cason, who felt that Justifying Fidel ought to have been a more appropriate title for the documentary.
Cason had invited Cuban dissidents to his home to watch the documentary broadcast on HBO and quoted them as saying they found it "insulting" that Stone had not personally interviewed the wives of jailed dissidents and had sent an assistant instead.
The diplomat said the message of Stone's film was that repression was justified in Cuba because the Bush administration was planning to invade the island.
"It’s the conspiracy theory that Stone has always had in his films," Cason said.
"The documentary is biased. I was disappointed, even though I was interviewed by his team," said veteran human rights activist Elizardo Sanchez.
Job for life
Stone asked Castro about political freedom and the future of Cuba, asking him if he were prepared to hand over to a younger generation of leaders.
"I think I will die on the job," Castro famously said, insisting he had no intention of pleasing US President George Bush by stepping down.
Castro said he had no intention of stepping down after 45 years in power. "I am not the one in power. It is the people who are in power," he claimed.
A year ago, Cuba rounded up 75 dissidents who were given prison terms of up to 28 years.
HBO yanked a flattering 2003 Stone documentary about Castro called Comandante because it failed to mention last year's crackdown on dissent. HBO asked Stone to go back to Cuba and interview Castro again.
A two-time Oscar-winning US director, Stone has a glittering filmography - featuring several movies with political content - that includes Platoon, Wall Street, Born on the Fouth of July, The Doors, JFK, Natural Born Killers and Nixon.