* AbandonShipping: The ending of ''J to X'' fullstop.
* BigLippedAlligatorMoment: In ''J to X'' there is a flashback episode where while the Marionettes are remembering their origins, Strawberry has a memory of her being berserker and gets dizzy. This is never brought up ever again.
* {{Anvilicious}}: ''J to X'' had such a blatant antideforestation episode that most viewers already got the message in the first five minutes.
* CanonSue: Marine from ''J Again''.
* LesYay: Marine [[LoveAtFirstSight imprints]] on Lime when they first meet, and spends most of ''J Again'' in a RomanticTwoGirlFriendship.
** BaitAndSwitchLesbians: [[spoiler:During her HeroicSacrifice, she realizes that her love of the oceans came from her awakening underwater -- meaning that her feelings for Lime were completely platonic, y'know?]]
* {{Macekre}}: Tokyopop's "translation" of the manga.
* MarySue: Marine, from ''Saber Marionette J Again''. She's not only stronger than all of the other marionettes, but has the extra ability to manipulate plasma, coincidentally making her the only one who can save the world. She hijacks the story, making the entire plot revolve around her. She easily makes friends with the main cast, despite previously attacking them in the forest and going around stealing everyone's stuff. Most {{egregious}} is the end of the series, where it is revealed that she has to sacrifice herself in order to save the world. Obviously she decides to do it, but Lime tries to stop her, even though doing so would condemn everyone on Terra II, even Otaru who she supposedly loves the most, to death (not to mention Marine would die anyway). This isn't just Lime being typically foolish, but everyone else agrees with her decision and tries to help her! Even though she fails to stop Marine from making the heroic sacrifice, it turns out that it wasn't much of a sacrifice after all, as Marine is only out of commission for a while but recovers just fine.
* {{Narm}}: Some of the English dub results in bits of this.
* UnfortunateImplications: The only homosexual character, Hanagata, appears as a cowardly and arrogant ButtMonkey who always gets LaserGuidedKarma whenever he acts like a jerk.
* VillainSue: Faust in the manga. Unlike in the anime, Faust never develops into a sympathetic character, never tries to atone for his sins, is never punished and to make it even worse... He achieves his goal!
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