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: Why didn't Thanatos' homunculi use magic against the escaping werecats?Answer: Richter, the first homunculus to chase them, was a special case. Thanatos even alludes to it being semi-unique.
Moral Event Horizon: Thanatos crosses it (in narrative) when he causes a major car wreck, killing at least a dozen innocent people, just to get at two teens. Technically earlier, though, he conducts freaky experiments on Salla, not the least of which involve tying her down and cutting her open. She states that the only reason he sedated her was to keep her from struggling too much.
Shikake's and Takeru's relationship. They go from snarking ruthlessly at each other to caring for each other like siblings (which they are). They have a very cute Vitriolic Best Buds thing going on and it's very realistic and nice.
Moral Event Horizon: If Sasuke didn't cross it when he disowned Nadeshiko, he certainly crossed it when he tried to kill Inou!
Nightmare Fuel: The description of Karin's body that is riddled with scars.
The death of Shusuke in "Interlude: Little Bird." Doubles as a Tear Jerker.
In an Adult Fear sort of way, the fact that Sasuke was willing to kill Inou in a duel because he thought he was too weak. Just the thought that Sasuke is so abusive that he would try to do that is terrifying. And think about how helpless Ino must've felt... And this scenario just gets worse when you realize that these types of parents and situations actually exist and happen...
Tear Jerker: Karin's reaction to Suigetsu's stillborn son. Until he gets better.
The entirety of "Interlude: Little Bird."
Ninako and her son Kumori. Her insistence that she doesn't want to see him again because she thinks he'll be a monster is really heartbreaking... It isn't until she actually holds him (even then, her eyes are closed) and feels him grab her finger that she finally sees him and realizes he's human.
The Woobie: Ooda. His crippling self-image issues alone - he explicitly calls himself disgusting and ugly - mark him as such, much less the trauma he's had to endure. And then there's the fact that he's the clone of most notorious criminals in the world, which he is painfully aware of.
Yakata as well. He's reviled and hated by everyone from his village except his parents on account of his abilities, pushed too hard by Sasuke, always nervous, apologizes a lot and even becomes the vessel for Orochimaru!
Ninako too. She's given a Caged Bird Seal, despite the fact that they're outlawed, on account of Hanabi's instability. When she gets pregnant with Hajime's child she's almost forced to choose between having the child aborted or drowned after birth. Even though that doesn't happen, and Hajime's allowed to raise the child, she falls into a deep depression that only worsens after the child is born and given away. She doesn't return to being her old self until she gets to see Hajime again.
Iron Woobie: Nadeshiko! Her entire family shuns her, as practically anything associated with her can and will trigger Sasuke's temper.