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.
Genius Bonus: The word "anima" means "soul, spirit" in Latin. In Jungian psychology the anima is an individual's true inner self, or soul.
Then there was the boy who fell in love with "the mermaid" (Husky had a fit over that), and Fly and Igneous (who never stops blushing). And, much more creepily, Fly's behavior with Cooro is... just, creepy.
Cooro and Shad in chapter 9. Cooro acts simply heartbroken for a long while when Shad kicks him out. Husky even seems slightly jealous about it.
Despite it not being direct Ho Yay, it's hard to get over the fact that Husky's opponent in the coliseum is a man named Dick.
Jerkass Woobie: Igneous. He may be prejudiced towards +Anima and Kimunle, but he has his (a little twisted) reasons and tries to serve his country with all his strength. At the end he (in a sense) loses two people he loved because of Anima.
Moral Event Horizon: When Cooro shows a tiny bit of free will Fly lies to him to crush the little bit of resistance Cooro built up.
There's also Magdala, who crosses this when she orders her pet lionesses to attack a boy who was caught trying to run away from the coliseum. The experience is traumatic enough to turn Sinon into a bird +Anima, and he quickly flies away.
Nana's past, particularly her father chasing her through the forest at night with a machete. The poor girl still has nightmares about it, and maintains a fear of being anywhere near a forest after the sun's gone down.
Also some Fridge Horror; Nana's safe, but her dad is drunk, irrational, has a deadly weapon, and is headed home where Nana's abused and exceedingly vulnerable mother is...
Cooro's birth. His mom died while pregnant with him and, following the custom of her village, was left out for the crows to eat. The crows start eating her and then baby Cooro bursts out of her stomach and flies after them.
No Yay: Fly's behaviour with Cooro is just creepy.
Some Anvils Need to Be Dropped: Don't discriminate against people just because they have something they don't want (this also applies to disabilities as well). They're still people just like the rest of you, and if you treat them bad, they'll treat you bad too. Basically: treat others the way you wish to be treated.
Tear Jerker: All of the kids' pasts, but special mention goes to... most of volume 10, really, and chapter 55 'Goodbye' in particular.
Also, Sinon's transformation into a +Anima. He thinks he's going to be mauled to death by lions, looks up, sees a bird in the sky, and just... reaches out.
Values Resonance: Despite the fact that nowadays there's more acceptance of people who are different (disabled, LGB Ts, etc.), discrimination, stereotypes, and wild misconceptions about said differences still run rampant, even to this day, and considering how realistically the issue was portrayed in this manga, this is all the more relevant today. The authoress was right to tackle such a sensitive issue as this, even if it was primarily a fantasy and published in the year 2000. We need more manga like this!
The Woobie: ALL OF THE MAIN CAST, for varying reasons. Nana's father abused her and chased her into the woods, and the group of girls she joined up with hated her because they thought she was showing off her +Anima powers, Senri had to not only watch his father die, but lose his right eye to the one who not only killed his dad but passed on his +Anima into him, causing Senri to supposedly be ostracized by the last of his clan for the fact that he turns into a monster whenever his eye-patch comes off, Husky was nearly suffocated to death by a crazy woman just because she wanted her son to have the throne and he spent a good chunk of his life away from his family, and Cooro for being born a +Anima, and because of that, he doesn't know what it's like to truly be human.