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.
Fridge Logic: Is there really a reason that the final battle couldn't have just taken place in a private rented gymnasium in the nearby city? It certainly would have removed ALL the convoluted plotting, betrayal, and trickery.
A possible answer: The Hifumi went to the hidden village to meet their grandmother and consider taking her up on her offer. They only decided to try the whole final battle thing after they were already there.
Iron Woobie: Kousukegawa becomes one over the course of the story. He stays pathetic, but is more than willing to put himself in harm's way, as well as face his fears, to protect his friends - despite being the only non-combat-trained main character.
Marty Stu: Tatsuya Rukawa. Some fans think he's pure awesomeness, others think he's the worst character for being a blatantly overpowered karate master who's good at everything and liked by everyone (everyone in-universe that is).
Thanks to living with the Gigi for several years, Hino has some interesting ideas about what makes for good eating, including scorpions, bizarre fish, and grubs and maggots.
Being from the Gigi tribe, Ginga has a similar idea of cuisine, once hilariously serving up some pigeon.
Nightmare Fuel: Despite the story generally being more on the light-hearted side, it still manages to deliver some frighteningly nightmarish moments, and not just limited to the more gruesome fights:
That Motoko is missing some of her childhood memories, especially regarding her mother, is not that really unusual. However all that she has recovered after Zero's return in Chapter 14-15 (as of Volume 9) is illustrated by blood-splattered panels, plus what seems to be scenes of a particularly gory carnage's aftermath, that seem to imply a more horrifyingly-traumatizing past than previously believed. Keep in mind that she's supposed to have been a freaking child (probably 5-8 yrs old) at the time. Yikes.
The sequence where Fujiko + Zero confronts Chou after he apparently guts Kosukegawa. It isn't just what she does to him (she double-kneecaps him, then shoots him in the shoulder and ear), it's her Dissonant Serenity while talking about how many bullets she has left and where they're going to go, with the faint hint of a Slasher Smile. Brrrrr....
Every time Zero shows up it's scary as hell. Bones are broken, people get shot, and limbs get torn off.
Tear Jerker: In chapter 49, where Motoko's mother's death and the circumstances in which it happened are finally fully revealed. Poor, poor kid, really.