Adaptation Displacement: To many a casual Studio Ghibli fan, it's fairly unknown that there even is a manga of Nausicaä, much less that it was made by Miyazaki himself. Although the movie is really just a 2-hour compression of the first quarter of the manga. It doesn't help that the manga only goes into print once every few years, if that.
Anvilicious: Of the Green Aesop variety, mostly for the film though. It gets a bit more complicated, if not somewhat subverted towards the end of the manga. Specifically, the question of whether or not the Master Computer's plan to artificially restore Earth's old ecology is just as bad as the callous environmental destruction that preceded it, since it would mean the deaths of the countless biotechnological creatures (including "Humans") who have made a life for themselves in the new world.
Nausicaä herself is much colder and more dire in the manga than in the movie, fitting for its more nihilistic tone, although she still ends up largely on the side of idealism. The fact that her real opponents in the manga are full-blown Omnicidal Maniacs, Master Computers, and whatnot means she also needs to have a little more steel in her will than her film counterpart ever has to muster.
Despite being uncut and more accurate, Disney's dub of Nausicaä still has its share of harsh detractors, with some declaring that it still fails to do justice to the original Japanese. You'll have to decide for yourself if you like it or not.
Fans tend to be split over the manga. Some consider it to be a vastly superior story to the movie; others think the plot gets too muddled and self-indulgent in the later volumes and prefer the movie's Adaptation Distillation.
Escapist Character: Nausicaä. Who wouldn't want to fly around the world in a miniature aircraft, exploring beautiful forbidden lands?
Jerkass Woobie: Possibly a number of characters, but perhaps most notably Kushana. Introduced in the film version as a seemingly stereotypical evil queen ("Nice valley. Think I'll keep it."), her status as an apparent Card-Carrying Villain is quickly subverted. This apparently was deliberate on Miyazaki's part — he describes Nausicaä and Kushana as "two sides of the same coin", largely differing in that Kushana has "deep, physical wounds".
Les Yay: In the manga, Nausicaä and Kushana have some of this going for them as Kushana seems to take a bit of a shine to Nausicaä as the story progresses.
Macekre: Warriors of the Wind again. The incident is why all Studio Ghibli licenses contractually require that not a frame of animation be altered or cut (with the obvious exception of translating the credits).
Moral Event Horizon: In the movie, the Torumekians (especially Kushana and Kurotowa) crossed it early on when they enslaved Pejite and assassinated King Jhil. However, the moment that seals them as barbaric and irredeemable warmongers is the invasion of the Peijite aircraft which was filled with children and the words that followed it:
"Leave no survivors!"
The Pejiteans themselves cross this line when they reveal that they intend to bait the insects into the Valley to wipe out the Torumekians there and wrestle back control of the Giant Warrior, an act that would also kill all of Nausicaä's people. Played with however, as it's the Pejite leadership that wishes to see this plan through while the civilians, with Asbel's help, elect to free Nausicaä rather then to be responsible for genocide.
The manga, full as it is of Gray and Grey Morality, doesn't have nearly as much of this, but there are a couple moments. For instance, when the Doroks are revealed to be manufacturing toxic mold to use its miasma to slaughter the invading Torumekian troops Ė Charuka pulls his HeelĖFace Turn once he realizes how insane that plan is.
Narm: In the movie, Nausicaä's (pink) dress gets soaked with Ohmu blood in the film and turns blue. Some earlier shots show the blood running down her and starting to change its colour slightly. However, it suddenly turns entirely blue after a quick cutaway - and the blood had apparently been so soaked it got her entire dress, yet none of it got on her skin or her hair. The fact that, despite the Ohmu blood soaking her clothes that fully, the logo on the front of her dress is still there.
It could easily be that the logo was of a different material that blood wouldn't stain (the red bit seems to be some sort of costume jewel). Also, in the manga, Nausicaä clearly has bloodstains all over herself.
Special Effect Failure: The film is one of the most beloved pieces of Japanese cinema ever, but it was also made before Miyazaki & co. got really famous, and was made on a surprisingly tight budget, so as a result there's a few places where... things don't quite work right. Blu-rays and super-large-screen theater projection in the 21st century can make these stand out a lot worse:
Especially at extremely high modern resolutions, a lot of the snow-like effects can be much more obvious post-production effects that don't mesh well with the actual scene.
At one point, our heroine escapes from the Pejite ship and is pursued by the Tolmekian corvette. One of the turret gunners attempts to fire on her... and at this point, the film ends on a surprisingly sad note, as the tracer rounds from the machine gun are clearly going straight into our heroine's torso.note She's actually fine, of course, and the film just plows on, but once you see it, you'll never again miss that the gunner is obviously hitting her dead-on.
Squick: Film-only example. When Kushana takes off her glove to show that she no longer has an arm and then says "Whatever lucky man becomes my husband shall see far worse than that." Ew.
She retains the armor on both her legs after taking off her armor, too.
Note that in the original manga, Kushana is 100% whole, as seen when she asks Nausicaä to help her put on her armor.
Word of Miyazaki states that Nausicaä's resurrection near the end of the movie was not meant to be analogous to Jesus and that he would have changed it if somebody had pointed out the similarities before the film came out Ė Miyazaki is many things; religious is not one of them. This may well explain some of the open discussion about the permanence of death (and how ways of avoiding it are explicitly unnatural) in later stages of the manga.