* AntiClimaxBoss: The Silver Samurai. Most complaints are about his overhyped feature in the film yet his single fight scene did not last long in the climax. And he's the modern PoweredArmor version, to boot.
** Some fans were rolling their eyes at the prospect of yet ''another'' Wolverine film, while others were more optimistic due to its change in director.[[note]]Although the problem [[ExecutiveMeddling doesn't seem to be the director]][[/note]]
** The decision to [[spoiler: bring back Wolverine's bone claws but still have an adamantium body]] has split fans in two. This isn't helped by [[Film/XMenDaysOfFuturePast the very next film]] [[spoiler: once again giving him adamantium claws without so much as an explanation]], creating a continuity error.
** The noticeable lack of mutants in the film, in favor of Japanese samurai has a lot fans divided.
* EnsembleDarkhorse: [[BadassAdorable Yukio]] is basically Logan's sidekick and she has acquired some remarkable popularity amongst the fanbase and movie audiences.
* FetishRetardant: Viper attempts to be a MsFanservice, but fails. This was due to a bad wardrobe choice, among other things.
* MoralEventHorizon: The villains go to great lengths for their cause:
** Shingen [[spoiler: puts a hit on his own daughter because his father named Mariko as the sole heir of the zaibatsu. The gang of Yakuzas in his employ are associated with Noburo, the corrupt Minister of Justice and Mariko's (arranged) fiance.]]
** Ichiro Yashida [[spoiler: fakes his own death to keep himself behind the scenes. He put the zaibatsu in near bankruptcy due to his obsession with Logan's mutant powers. He then uses the armor to steal Logan's healing factor. Harada had been the faithful servant who guarded Mariko, who ended up getting killed by Yashida's madness.]]
** [[SpecialEffectFailure The freaking bear.]]
** Logan jumping over the guy on the bullet train, whilst ''screaming''. Try not to laugh.
** During the climax, Viper chases after Wolverine and Mariko, and hisses as she does so. Both her run and the hiss look and sound ridiculous.
* TheScrappy: Viper, with any semblance of being a MagnificentBitch taken by [[spoiler:Yashida himself]], leaving her an enormously bitchy SmugSnake with FetishRetardant. Didn't help her case when Viper's characterization here gives her snake powers.[[note]](she didn't have any in the comics, as she was originally "Evil Black Widow")[[/note]] As a final punch to the gut, she has absolutely ''nothing'' to do with her comic book counterpart.
** It's quite obvious that the train action scene is filmed in front of a green screen.
** The Silver Samurai suit doesn't look as convincing as it should be, considering how well-rendered armored battle suits in movies like ''Film/IronMan'' are nowadays.
** While the digital bear at the beginning of the film is somewhat hokey, the practical-effects created bear that appears shortly afterward just screams animatronic.
* StrangledByTheRedString: Logan constantly dreams about Jean Grey and wishes to be with her again yet he shares a few intimate moments with Mariko, who already engaged to another man at the time and only knew him for a few days. The film noir setting could justify this relationship as a form of comfort for Logan.
** The bullet train fight sequence.
* SurprisinglyImprovedSequel: Initial reviews seem to be placing it as one to ''X-Men Origins: Wolverine''. It can also be considered one to ''X-Men: The Last Stand'', since ''The Wolverine'' takes place after [[spoiler:Logan was forced to kill Jean Grey]], but it's more contentious to say so as it's not ''really'' an X-Men film and ''X-Men: First Class'' was also well received.
* TearJerker: The scene where Logan kills the bear. The bear literally asks him to put it out of its misery and Logan. Imagine him reliving the moment when he was forced to kill Jean.
** The decision to have the Silver Samurai [[spoiler: be the old BigBad guy, when they had TWO characters who could have made for a really Badass PoweredArmor warrior for Wolverine to face and have a real adamantium fight with (those two being Harada and Shingen).]]
** The design itself means the climax devolved into a generic superhero CGI fight, that really didn't match the film noir tone the film had. Most people would've preferred Wolverine fight a [[spoiler: human-sized]] Silver Samurai.
* WinBackTheCrowd: The film ([[BroadStrokes mostly]]) discarded the previous ''Wolverine'' film and basically started from spin-off scratch, adapting one of the most famous comic arcs for the character and going for a smaller and more personal scale for the character. The result was far more well-received than ''Film/XMenOriginsWolverine'', enough for Fox to kick the tires on a follow-up with Hugh Jackman and director James Mangold returning.