These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
People are still pissed that this lost Best Picture to Kramer Vs. Kramer. To be fair, that film is great in its own right. It's comparing apples and oranges... a great family drama to a great (anti-)war movie. In any case Apocalypse Now is pretty much frequently ranked as one of the best films of all time and the best war movie ever.
Robert Duvall's loss for Best Supporting Actor could also be seen as this. Granted, Melvyn Douglas was great in Being There, but Colonel Kilgore has unquestionably become a more iconic figure in American cinema (with some referring to it as the best performance of Duvall's career).
Martin Sheen also failed to earn a Best Actor nomination.
What the helicopter raid on the village was intended to be. What the viewers saw it as,however.... The village probably qualifies as a legitimate military target, as it's stated outright to be a Viet Cong outpost, and even has several female combatants throwing a grenade into a medivac chopper, but then again the actual reasons for the attack (Colonel Kilgore and his bloody surfing) demean it all.
The Viet Cong's mercifully offscreen hacking the limbs off children who received vaccines from western doctors.
Older Than They Think: The premise of the movie, as well as the famous line, "The horror... the horror...", are taken directly from Heart of Darkness.
One-Scene Wonder: The movie gets summed up as Robert Duvall showing up with his Wagnerian helicopters and other Crazy Awesome antics, and then Brando emerging from the shadows and monologuing. Reportedly, there's some other stuff in the middle too.