Angst? What Angst?: In her introduction, Hinata is manipulated by her father, who uses her desire for his love to do so, into becoming a serial killer, betraying her new friends, having her closest friend almost die, and then having herself almost die, only for her father to then reveal he was lying to her the whole time, after which he is promptly shot dead.None of this is ever referenced again, and Hinata carries on as a normal girl who shows no sign of stress or trauma from that experience.
Broken Base: The English dub voices of Yukiteru and Yuno. Some fans think their English voices are terrible and don't fit their characters, other fans think that not only does the English voices perfectly fit their characters but also makes it a refreshing change of pace from the high-pitched girly voice and shy, insecure, young boy voice that have been overused a lot in anime.
Complete Monster: Funatsu, though a minor villain, caused one of the most horrific events of the series. Once a member of a peaceful cult based around a young girl, Tsubaki Kasugano, who allegedly had prophetic powers. Funatsu killed her parents when they planned to disband the cult, fearing losing his power. Becoming the de facto head of his reformed cult, Funatsu allowed the members to rape Tsubaki regularly, possibly taking part himself, and drugged her to keep her defenseless against their constant assault. So intense was Funatsu's cruelty to Tsubaki that she went insane and began plotting to destroy the world.
Yomotsu Hirasaka, though that's kind of inevitable for a blind insane Super Sentai parody.
Crosses the Line Twice: Takao Hiyama appears in a flashback in the middle of one chapter... only to take a spear in the back, courtesy of Yuno. Him being an Asshole Victim is probably what makes it so funny in the first place.
Darkness-Induced Audience Apathy: In a similar vein to Elfen Lied, the series has drawn a lot of criticism for its constant barrage of dark backstories for Villain of the Week characters that get killed off at the end of their arcs anyway and the grimdark storytelling exhausting itself after awhile to the point where it's just shock value.
Draco in Leather Pants: The more avid fans of Yuno tend to tone down her more negative and violent qualities in favor of her devotion to Yuki.
Similarly, Minene Uryu has some fans who see her as a hero, selectively ignoring the fact that she's a violent terrorist who will kill anyone, even children, with little remorse.
Die for Our Ship: Both Yuno and Akise are victims of this, though the latter has it more prominently within the fandom. Notably, it actually is in-character for Yunonote the main one from the first world, anyway - her second and third world counterparts, not so much to kill people that come between her and Yukiteru, though it's more often this trope than Murder the Hypotenuse.
Who knew that Rick and Morty would share a plot point with this, of all things? In both, a major character goes into an Alternate Timeline to try and fix a mistake, and ends up killing that timeline's version of themselves to ensure their cover.
The Netflix Death Note film also causes some of this; the changes to the protagonists make them more reminiscent of Yuki and Yuno than of Light and Misa.
Magnificent Bitch: Mur-Mur is the humorous minion of Deus Ex Machina, but schemes behind her master's back to continue the survival games for eternity to amuse herself. Convincing Yuno Gasai to travel to the 2nd World and take that Yuno's place so she can still be with Yukiteru Amano, Mur-Mur would also take her own 2nd world counterpart's place so she can manipulate the people in that world; She tells Keigo Kurusu that he can cure his son's illness if he wins causing him to turn against Yuki, and lies to Yuki that he can resurrect his dead parents if he becomes god. Mur-Mur also takes direct manners to those that interfere with her plans such as erasing all of Akise's actions in Paradox, abandoning Yuki in the 2nd world before traveling to the 3rd world with Yuno, and brutalizing Minene Uryu when she fights her; she would have won if Yuno had not killed herself out love for Yuki, leading Mur-Mur to unite Yuno's 3rd world counterpart with Yuki.
Tsubaki crosses this when she orders her followers to strip off Yuno's clothing... and to gang-rape her, all so she could lure Yukki out of his hiding place. This one is a particularly sad example, since given Tsubaki's own Rape as Backstory, it's clear that she has become so desensitized to sexual violence by this point that she would casually threaten it against someone else.
Mur Mur crosses this when she undoes the positive future in Paradox by deliberately erasing everyone's memories and goes back in time to make sure that the 2nd is still alive and kills them all. She also uses the wounded Yuki to prevent Akise from stopping her plans.
Akise in the manga crossed it when he abandons Yuki's friends to let them die by Yuki's hands, just so he can get the chance to kill Yuno. Even Yuki is disgusted by this. Defied in the anime, where he actually tries to stop Yuki.
The English covers. "Every text could be your last."
The soundtrack in the anime often uses stock music stings heard in various others shows (such as Cyberchase) for dramatic scenes, torpedoing any tension to oblivion. One such moment is The Reveal in episode 3.
Rooting for the Empire: Plenty of fans were rooting for some of the other Diary Holders (like Minene or Yuno) to win instead of Yuki, seeing as how they came off as more sympathetic and likable.
The Scrappy: Yuki's three "friends", for being irrelevant following the storyline that involves them but still showing up, for being non-Diary holders trying to impact the game, and for generally being Too Dumb to Live. It doesn't help that half the time they claim to be on Yuki's side, they're actively plotting against him. Unlike Akise, their leader, who is later revealed to have a very good reason for finding out about the Diary game, they are never given any such reason. Special mention goes to Ouji Kosaka, who has an unpleasant and unlikable personality in addition to his stupidity.
Kurou Amano probably is the worst offender of this trope in the series, as after making a deal with Yuki's enemies to destroy his diary, stealing a parachute and leaving his son to die, and stabbing his ex-wife, Yuki's mother, to death in order to stop her from alerting the police, the story suddenly has him break down in remorse over it all, with him being Easily Forgiven by Yuki. The fandom, on the other hand, was not so forgiving.
Viewer Gender Confusion: Orin, the second-in-command of the children in Eighth's orphanage, is confirmed to be a girl in Mosaic.
The Woobie: Second World Yuno. Yes, her stalking Yuki is kind of reprehensible, but it's never taken to the extremes that her First World counterpart goes to. Her Freudian Excuse is explored in detail more than the previous Yuno, and unlike the next Yuno, she doesn't live long enough to see a happy ending, getting killed by her previous incarnation without knowing why.