“At the heart of science is an essential balance between two seemingly contradictory attitudes — an openness to new ideas, no matter how bizarre or counter-intuitive they may be, and the most ruthless skeptical scrutiny of all ideas, old and new. This is how deep truths are winnowed from deep nonsense.”
― Carl Sagan, The Demon-Haunted World (1975)
This list represents a growing collection of documentaries in need of a good debunking.
This is a controversial list, and there will likely be entries here that you disagree with. But, before you post a lengthy manifesto that I probably won't read, try looking up the film in question on rationalwiki.org, or maybe Google it, followed by the words 'debunked' or 'fact checked'.
And if you still disagree, that's cool. If it makes you feel better, I actually have a film on here that I mostly agree with ('The Magic Pill'). It's been  heavily criticized by the Australian Medical Association,  it makes some bold claims and  it doesn't do a good enough job of defending its position with current nutritional science, so I've listed it here.
Netflix Is The Last Place You'll Find A Pro-Science Documentary, via the ACSH:
Watching a Documentary Does Not (Necessarily) Make You Smart, via jordandetmers:
Notes on Bad Documentaries (Or, Can a Documentary Be So Bad It’s Good?), via Filmmaker:
Streaming Services Have a Conspiracy Theory Problem, via Slate:
Doc or Crock: 6 Recent “Documentaries” Accused of Being Fake, via the AV Club:
There Is Almost No Good Science in the Movie 'What the Health', via Vice:
That *#^% Sugar Film, via Slate:
6 Famous Documentaries That Were Shockingly Full of Crap, via Cracked:
Debunking 'What the Bleep Do We Know', etc., via LudicFallacies:
'Forks Over Knives', is the Science Legit?, via Denise Minger:
Unfairenheit 9/11, The Lies of Michael Moore, via Slate:
Correcting the 'Fed Up' Record, via foodinsight.org: