Just like Michael Moore with Farenheit 911.
There's a difference.
For one thing, Stone never claimed it to be the truth. It was a drama and he said so.
The second thing is, that some of the stuff probably 'was' true, or at least was leaning in the right direction.
If you think Oswald killed JFK, there's a bridge in brooklyn I'd like to sell you.
I think it's more likely that Castro or even LBJ himself had it done then some giant conspiracy with virtually everybody involved done for the sake of the military industrial complex, but I'm not so naive to think we know the whole story.