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.
YMMV: Brave Story
The book and its direct adaptations contain:
Fridge Brilliance: When Wataru becomes a Highlander, he is told that the Highlander's Wyrmband will sear the skin of any wearer who strays from the path of justice. so why does it remain dormant when Wataru murders the lookalikes of his father and Rikako Tanaka in the Swamp of Grief? Because the ways of Vision are defined by Wataru's heart and mind, and Wataru subconsciously believed that what he was doing was right at the time.
Ho Yay: Wataru keeps following Mitsuru, even after it's revealed that Mitsuru is a jerk. Throughout the whole book, Wataru acts more like a girlfriend than a frenemy to Mitsuru.
The movie takes this and ramps it almost Up to Eleven. It's the main cause of all of the doujinshi floating around.
It's not exactly hidden in the book:
"He had noticed Mitsuru's eyelashes then — long like a fashion model's"
"He's got a pretty face, like a doll."
Jerkass Woobie: This might be too sympathetic for Mitsuru in the book, but he qualifies as this in the movie.
Tearjerker: Kutz's death, obviously, but also Mitsuru's, so very much. The former does not apply to the movie due to a case of Spared by the Adaptation, but the latter definitely does.
The Woobie: Meena seems to fake this in the manga. Turns out that she's real.