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.
Ass Pull: During the Hunt for the Arm Arc and after you get the feeling that the story is just making up a lot of the things that happen on the fly and heavily RetConning a lot of the past rules and statements mentioned before (such as Sakura and her father being Last of His Kind, the overuse of one's ability will kill them, what one's powers is capable off, and the level system of the Code:Breakers where the numbered ones are supposed to be the strongest). It almost feels like the manga was supposed to end with the death of Rei's brother but decided to keep going so it needed to do a lot of changes to do so.
Ho Yay: Just a bit, but it might be due to the translations. Calling someone "loved" or "beloved" in Japanese can be surprisingly more platonic than in English. That being said, it's definitely still there.
Yuuki: My...My true feelings for him...are a whole lot stronger...than yours...
He's saying this as he tries to kill Ogami, the guy in question who Yuuki's referring to in that quote. It's...complicated.
Heike fanboys over the Code:Emperor. But, considering he seems to want to kill him now.... there's a pattern here isn't there?
Jerk Sue: Arguably Ogami is this. He forces his opinion on others and call them trash. If things aren't looking to good for him and he seems to be losing an argument, other characters quickly are there to play his advocate and defend him.
Mary Sue: Sakura. Loved by everyone at school, gets amazing grades, is a martial arts expert, is immune to all Code:Breaker powers...one could easiily mistake her for a bad Fan Fic character.
Moe: Sakura's mom: she's the size of a small child and loooooves playing dress up since she's Sakura's adopted mom, who knows how old she is (though when Sakura was shown in a flash back as a little girl, she looked the exact same). Sakura's biological mother is just an older version of Sakura. There's also Sakura's schoolmate Nenene, who is also very tiny (yet two years older then Sakura), has glasses, and loves groping Sakura's breasts (she even names them).
Chibisakura, who looks more like a stuffed toy than a child who has fatal power-nullification powers and doesn't see killing as a "thing". Ogami laughs at the idea of Sakura being a threat.
Nausea Fuel / Fridge Horror: The Vega-expy murderer left diamonds with his victims' neatly sliced corpses; it's later revealed he can spit gems... I mean, that was spit, wasn't it?
Too Cool to Live: Emperor-dono, we hardly knew ye. And probably Code:Seeker (AKA "The one being sought" AKA Ogami's brother) and Hitomi (Ogami's mentor), who were both killed at the end of their arcs.
True Neutral: Sakura's parents stayed out of EDEN's business to ensure that Sakura grew up normally and to preserve peace between power-users and Rare Kinds. It seems that the President's school is filled with such students, not just the moles from EDEN and Re-Code.
Unfortunate Implications: Sakura with Rei: no matter how cold a guy is to you, no matter how easily he snaps at you, no matter how many times he tests you, keep doing everything you can to be with him. Because time and the Power of Love will change even a cold serial killer no matter how many times you have to do so.