Given the fact that the mangaka doesn't like smart characters, it shouldn't be too surprising that Naruto has its own page here.
Warning: Unmarked spoilers on this page, particularly in "THE PAST" folder.
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Twenty years ago Rin is kidnapped by the Mist and the three tails is implanted into her, and she's "chased" back to Konoha in the hopes that the three tails would bust out and wreck up the joint when she arrived. You'd think: That she'd turn on her "pursuers", stop moving, or run in the opposite direction. Anything to buy time for Minato to arrive and try to properly seal the three tails so it couldn't escape. Even if Minato hadn't been able to do anything, it was still a better option than what she did. Instead: She makes Kakashi kill her, kicking off the entire series.
Naruto is the son of the 4th Hokage and the Kyuubi's previous jinchuuriki. You'd Expect: Those who knew this — Sarutobi, Jiraiya and Kakashi — to take extra special care in Naruto's upbringing and raise him. That they would at least train him better, ensure that he had better treatment in the village, and that when he was of appropriate age, inform him of his parentage to encourage him. Instead: Jiraiya doesn't even associate with Naruto until he's nearly a teenager, Sarutobi hangs in the background without taking necessary measures, and Kakashi says nothing. It is through a series of contrived coincidences occur that reveal the truth to Naruto, when learning beforehand would have been very helpful. Fridge Horror: This becomes very jarring in the movie Road To Ninja, when Sakura is praised as the hero's daughter, due to her father being the hokage in the movie's alternative universe. Additionally: This same type of abusive upbringing is what turned Gaara into the dangerous psychopath he is when he's first introduced. There was nothing stopping Naruto from abandoning or betraying the village when he got to a certain age aside from Naruto's own personality.
The Kyuubi attacked Konoha and killed many people. The fourth hokage heroically sacrificed himself to seal it into a newborn baby. However, the child now has no family to speak of, and should he let it, the beast will take over. You'd Expect: The people of the village to raise the child positively, and keep loving people around him, if only to monitor him. Because the last thing you need is someone with a Super-Powered Evil Side with mental issues. Instead: They are outright hostile towards him for something he didn't do, leave him on his own with no real adult supervision in his life, and encourage their children to do the same. All without ever telling him why.
Sarutobi has to break the news of what happened to the Kyuubi and the Yondaime to the village. You'd Expect: He (lies and) tells them that the Kyuubi died with the Yondaime and Naruto is the Yondaime's son asking the village to help raise their hero's son. Instead: He tells them the truth (except the Yondaime's son part), forbids people to talk about it and then does nothing as Naruto experiences the worst childhood ever. Even worse, he does nothing to help make Naruto's life better yet has the gall to feel guilty about it.
A few years before the start of the story, Itachi Uchiha was given a mission to wipe out the whole of the Uchiha Clan, to prevent them starting a civil war. Itachi agrees, but is unwilling to kill his beloved little brother, Sasuke. He also wants to ensure Sasuke's survival and dispel the Uchiha's negative reputation it gained following the Nine-Tails attack. You'd Expect: That Itachi would use either genjutsu or transformed shadow clones to make it look to Sasuke like a load of foreign ninja carried out the attack, and that Itachi killed them all. That way, Sasuke, while still having lost much of his family, wouldn't have anyone he could take revenge on, and he'd have a loving brother who could help ease his pain, therefore giving him a lot less reason for his Face-Heel Turn. As for the rep problem, he can then encourage Sasuke to work on proving it wrong, similar to what Naruto does for most of the series. Instead: He tells Sasuke that he was responsible for the attack, makes himself out to be a monster, and Mind Rapes him for good measure, before running. He does this in order to give Sasuke motivation to hunt him down, kill him, and therefore redeem the Uchiha. Result: This scheme ends up working a little too well, before failing completely: In order to become strong enough to kill Itachi, Sasuke ends up defecting from Konoha to Orochimaru, a guy who wants to possess him for his eyes. And Sasuke happily embraces the possibility of this happening if it would help him get his revenge. When Sasuke does kill Itachi, he's taken into the custody of the Big Bad, who explains the truth of what Itachi was up to, causing Sasuke to want to destroythe whole of Konoha.
The selection process deserves mention when it comes to Team 7. You'd Expect: For Iruka (a man who has taught these kids for years) to point out that putting an Ineffectual Loner with revenge on the brain, an emotionally abused Attention Whore who always picks a fight with said loner and a fangirl of the loner who keeps beating the Attention Whore on the same team is a bad idea. Instead: The team is put together and it's a train wreck at first. It gets better...only to devolve when Sasuke gets jealous of Naruto.
As part of Team 7's first team exercise, they're told to steal some bells from their sensei, Kakashi. After a pretty impressive attempt by Naruto to steal the bells nearly succeeds, Kakashi disappears from his immediate area. Naruto later sees one of the bells just lying on the ground near a tree. You'd Expect: Naruto not to fall for the oldest trick on the scroll, and either ignore the bell or have a shadow clone pick it up. Instead: He assumes that Kakashi dropped the bell and tries to take it, and predictably gets caught in a snare when he does so. As Kakashi states soon afterwards, "If the bait is obvious, don't take it".
In the Forest of Death during the Chunin Exams, Sakura is left fighting 3 sound ninja all by herself. She tricks one of them through an admittedly tricky series of substitutions, getting him to assume she's a substitution when she isn't, giving her a window of opportunity as she jumps down on him with a kunai in her hand. You'd Expect: She'd jump on top of him and stab him with the kunai either to kill or disable him so he couldn't fight her anymore. Instead: She lands on him and bites his arm, doing nothing while he repeatedly punches her on the head.
Before THAT bit of stupidity occurs, Lee intervenes to save Sakura from the three ninja. He has the choice of either taking off his ridiculously heavy leg weights, greatly increasing his speed to Flash Step levels, or using an uber-move that will only work on one person, and will render him unable to fight after performing it. You'd Expect: Lee to take off the weights, and use his speed to get within range of the Sound Nin and punch them out. Instead: He uses the uber-move on ONE of the three ninjas, and can't fight effectively afterwards. To make matters worse, the guy he uses it on is unaffected, thanks to his teammate, making Lee's actions pretty much a stupid sacrifice.
Also during the Chunin Exams, Sasuke gets the Cursed Seal from Orochimaru. Kakashi finds out, and decides to deal with it. With little other option, he does the sealing himself, using a seal that is dependent on Sasuke's willpower to maintain. You'd Expect: Kakashi to have noticed that Sasuke is desperate for power to defeat his brother and will jump at any opportunity to get it, and do his best to find a better solution to the Cursed Seal issue. Instead: He teaches Sasuke Rock Lee's Flash Step as well as his (Kakashi's) signature move, so that he'll have techniques other than the Cursed Seal to rely on, but aside from that he does absolutely nothing. It seemingly never occurs to him that these alternatives to the Cursed Seal might not be enough to help Sasuke. It goes without saying that this strategy didn't really work too well. Worse Still: While checking on Sasuke, no one makes an attempt to check on Naruto. You know, the kid WITH THE NINE-TAILED FOX SEALED IN HIM! Jiraiya only checks when he trains Naruto a few days later.
Another for the Chunin Exams, Sound Ninja Dosu Kinuta has realized that he and his teammates have been set-up and used as fodder against Sasuke by Orochimaru and vows to himself to not let this treatment of them go unavenged. You'd Expect: Him to try and somehow get information to Sarutobi about what his former student is doing so that Konoha can make preparations to stop Orochimaru's planned attack and foil it. Granted, Sarutobi might not believe Dosu's word, but Dosu doesn't know that for certain, and in any case changing sides would be a lot safer than continuing to work for Orochimaru. Or: He could try to sabotage Orochimaru's plans by going to Zaku and Kin at the Hospital after the drawings and getting them out of there before they are retrieved by him. With them gone Orochimaru has no people to use for Edo Tensei and he has to find new sacrifices. Instead: He decides to go challenge Gaara, a guy he's seen personally crush and cripple Rock Lee, so that he can be in with a better chance of fighting, and presumably curbstomping Sasuke tomorrow, just so he can spite Orochimaru. He gets killed in ten seconds, not only making his realization pointless but also wasting a character who could've been a wildcard for people to not know whose side is he on.
Gaara's father needs to insure that he has control over the Shukaku to make sure that he won't lose control of him. You'd Expect: Him to wait until Gaara is older and make sure that he's being treated fairly to keep him and Shukaku in control. Instead: He has his uncle betray him, lie to him and say that his mother never loved him and then try to blow him up... And he had already been having a horrible day already. Not to mention he was only six years old!Any six-year old child would have little control of their emotions! Idiotic Jerk Ass...
After the revelation that Itachi is trying to protect Sasuke and wants him to be loyal to Konoha. After Sasuke confronts him and Kisame. You'd Expect: Itachi to hold his cover and to do as little damage as possible. Instead: He uses Tsukuyomi to force Sasuke to relive the Uchiha massacre again (having done the same thing to Sasuke immediately after it happened). End result: Sasuke defects from Konoha and later plans to destroy it and everyone in it. Good job, Itachi.
Sasuke's no better in that scene. He knows, among other things, that Itachi had made ANBU before Sasuke even graduated from the Academy, and that he has YEARS more experience than Sasuke, not just because of age, but because Itachi's ninja career started when he was 6 (Sasuke's started at 12 or 13). You'd Expect: Sasuke to realise that he's outmatched either way, and to not try anything stupid. Instead: Sasuke tries to charge him head on, and is easily beaten and hit by the aforementioned Mind Rape as a result.
Naruto is having trouble hitting Kabuto with his new uber-move because Kabuto's too good at dodging and is kicking the snot out of Naruto despite only having one working arm. Employing desperation tactics, Naruto manages to grab Kabuto's good arm. You'd Expect: That Kabuto might remember that he still has legs, and kick Naruto in the face. Instead: He spends almost half a minute doing nothing but standing there tugging ineffectually at his trapped arm, watching as Naruto charges up his uber-move and smacks him in the chest with it. It having been established that A. Rasengan has a fairly long build up time and B. Even if it didn't it only moves as fast as Naruto can throw a punch... And Kabuto is on the high end of skilled, AGILE, and quick witted ninja.
The first fight at the Valley of the End has Naruto and Sasuke make their final attacks. Both pretty much waste any actual killing force, limiting them to knockout strikes. Sasuke's now normal punch is aimed for the gut. You'd Expect: Naruto, who's aiming for the head, to knock Sasuke's ass unconscious. Naruto knows he's going down, too, but at least Sasuke wouldn't be going anywhere. Instead: He decides to graze Sasuke's forehead protector. Apparently since Sasuke said he couldn't do it.
The fillers did this with Neji in the Hoshikagure Arc. Big Bad Akahoshi hires the heroes to protect the village's secret weapon, but then takes measures to recover it himself, then declares them enemies of the Hidden Star Village, in front of a large crowd because they know of their motives. In the finale, everybody comes together, Akahoshi's plan to mutate the children of the village with the power of the meteorite into an army that will help him conquer the other nations is exposed, and he decides to use the meteor by himself to slaughter his own people and the Leaf genin present. You'd Expect: For Neji to recognize an open declaration of war, and coordinate a joint attack taking out the bastard. Instead: He forbids his team to interfere in another country's internal affairs - basically condemning an entire village and his own teammates to certain death.
Filler Neji again. During the penultimate filler arc of the original series, Menma Arc, Naruto escorts an amnesiac ninja to the Land of Rice Fields, to help him recover his memory. Neji is ordered to follow them and keep an eye on the latter, due to strong evidence of him being a sound ninja, and his possible connection with the man who attacked the village. They arrive to a village near the Land of Rice Fields that has been burned to the ground by sound ninjas, and there's a good possibility they might return at any moment, killing many innocents. The amnesiac Menma decides to stay and help the people defend themselves. You'd Expect: Neji to agree, seeing how his mission was to keep an eye on Menma, and not much else, also considering the possibility that there might be a connection between the ninjas who attacked the village and the one who was after Menma, not to mention that Menma was found shortly after the attack on the village took place. Instead: He refuses to stay and urges Menma and Naruto to carry on with the mission, even after Menma tells him that helping the villagers might trigger some of his memories and refuses to even look into any possible connection between Menma, the village, the attackers and the man who attacked the leaf village earlier, effectively defying the Hokage's orders because of a minor technicality.
During the mission to rescue Gaara from the Akatsuki, Team Kakashi and Team Guy arrive at one of their hideouts. They have very strong reason to believe that both Gaara, and a pair of Akatsuki members are in there waiting. They also learn that to actually get into the hideout, they have to remove five seals, one of which is on the entrance, the other four scattered around the surrounding environment, all at the same time. Also, Naruto's with them, and he can duplicate himself hundreds of times over. You'd Expect: That Naruto would create four copies of himself, have them remove the other four seals before poofing away. That way, both teams would be in position to fight the Akatsuki. Instead: Team Guy goes off to deal with the seals, leaving Team Kakashi to deal with the Akatsuki alone. Worse: The seals create copies of the people who removed them, that match them in strength, techniques and endurance. The result is that Team Guy are kept distracted for a long period of time, and therefore unable to help anyone, whereas if they'd used Naruto's clones, they could have just one-shotted the copies of them if they got too close.
At the end of the Sai and Sasuke Arc, Team 7 has just confronted Sasuke, with their primary goal in training being to take Sasuke back to Konoha. You'd Expect: That Naruto would do what his video game incarnation did, and try to take back Sasuke by force. Even if he's easily outmatched, at least their training wouldn't be a waste of time. Instead: He hesitates and, aside from one attack, doesn't even attempt to fight Sasuke. The result, a Shaggy Dog Story for Naruto, as all his training comes off as a complete and utter waste of time.
At the end of the Hidan and Kakuzu arc, Akatsuki member Kakuzu is incapacitated after being outwitted by Naruto. Kakashi kneels beside him and gives a speech about the new generation surpassing the one before it. You'd Expect: Kakashi to restrain Kakuzu, and have Ino try and fix him up. Then they take him back to Konoha, and question him about the Akatsuki. Instead: Kakashi kills him. What makes this moment worse is that in the next arc, Konoha is hoping to get information about the Akatsuki. Speaking of that... You'd Expect: Tsunade to have Hidan, who was blown to bits and buried alive dug up, then have what's left of him questioned. Instead: She doesn't, and decides to order three squads worth of ninja to try and capture Itachi. Admittedly, this does have the additional purpose of providing Konoha with bait for Sasuke, should it succeed, but as for finding out about the Akatsuki, there was no excuse for her not having Hidan questioned.
Anime filler. Sasuke and Suigetsu have stormed a castle to get their hands on the Executioner's Blade. After Sasuke convinces him not to kill the lord of the castle, Suigetsu then slices the castle's main support beams, and tells the lord that the place will collapse soon, and that he should get out if he wants to live. You'd Expect: That the lord would run for it as soon as it became clear that Sasuke and Suigetsu weren't going to kill him. Instead: He just kneels at the foot of his bed, screaming as the castle collapses around him.
During the Itachi Pursuit Arc, we learn that Jiraiya has access to a technique called Sage Mode, which enhances the user's physical abilities as well as their jutsu. One arc later, Naruto is able to learn this technique within the span of a week, and in fact manages to surpass Jiraiya in it. He doesn't have to do anything special to be able to start learning it either; the only requirement for the student is that they have a large amount of chakra, which Naruto easily fills. Now let's go back to the two and a half year training trip Naruto went on with Jiraiya, which Naruto undertook for the sole purpose of becoming strong enough to both bring Sasuke back and defend himself against the Akatsuki. You'd Expect: Jiraiya to have Naruto trained in using Sage Mode during the trip, so that he'll have the skills necessary to fulfil his goals. This would really have been a good idea after it became too dangerous for Naruto to use Kurama's chakra because of how weak the seal had become. Instead: He doesn't, and as a result, Naruto has to fight much harder battles, and the first time he meets Sasuke after the Time Skip, his former teammate easily overpowers him.
Right before Naruto starts his Sage Mode training, we learn that the toads can summon their summoners (reverse-summoning). Now let's go back to Jiraiya's fight with Pain in Amegakure; Jiraiya gets out-gambitted by his opponent, loses his left arm and gets his throat crushed. It becomes clear that the fight's lost, and Jiraiya has the toads flee. You'd Expect: The toads would have reverse-summoned Jiraiya out of Amegakure, and then taken him to Konoha to get his injuries treated. The current Hokage is an extremely capable healer, and it's not as if anything bad would happen if Jiraiya fled this fight. And this way, he'd be able to pass on more information on Pain. Instead: The toads do nothing of the sort, and aside from giving Konoha one hint about the nature of Pain, Jiraiya dies a pointless death.
Nagato/Pain has a pretty big one. It's plainly evident for all to see that he could have succeeded in kidnapping Naruto at one point, and indeed that was the entire goal of him going to Konoha in the first place. You'd Expect: Him to, you know, do so. Instead: He decides he wants Naruto to be juiced up by the Kyuubi chakra when he defeats him (even though he already had Naruto NAILED TO THE GROUND with his chakra disrupting black spikes), so he stabs Hinata in the chest, pretending to kill her, just to piss Naruto off. End result six-tails and an ass-whoopin' courtesy of Naruto.
More anime filler. In episode 183, Tsunade believes that Naruto is carrying a virus that affects chakra, and fears that it may ruin things for the village. She decides to have Naruto go to the hospital and get checked. You'd Expect: Tsunade to first try and PERSUADE Naruto to go the hospital. You'd think they wouldn't need to say much, other than, "Naruto, we believe you're infected with a virus that could cripple the village, so would you mind reporting to the hospital?" Instead: She orders a load of ninja to capture Naruto and take him to the hospital, and none of them think to just tell Naruto what's going on. As a result, he runs, and refuses to let them capture him, and the issue takes far more effort than needed to be resolved.
In the same episode, Naruto tries to evade everyone trying to grab him by creating a load of shadow clones. Three large groups of them run into Kiba, Choji and Tenten, who attack them. You'd Expect: The clones to at least have the sense to try and avoid getting hit. Instead: They just stand there like lemmings without making any attempt to defend themselves, and are poofed away quite easily.
Sasuke is confronting Danzo for ordering Itachi to slay the Uchiha clan. Sasuke, not fully trusting Madara's story, asks Danzo if this is truly the case. Danzo's mind control eye has not fully recharged yet. You'd Expect: Danzo would stall for time until the eye is usable again and use it to bring Sasuke back under control. Instead: He confirms Madara's story, fueling Sasuke's rage.
Sakura has resolved to kill Sasuke herself, and is travelling to his location with Kiba, Akamaru, Sai and Lee. Unbeknownst to the three of them, Sakura has come up with her own plan to take Sasuke out. You'd Expect: That she would tell her teammates about this plan, and try and get their support. That way they can back her up if something goes wrong. Instead: She uses knockout gas on them to keep them from interfering. As a result, when the plan goes wrong, she only survives due to Kakashi and Naruto coincidentally being in the nearby area.
Sasuke has just given Karin the nth degree when Sakura shows up, supposedly wanting to join him in his nefarious plans like she proposed in Part I. Sasuke is still standing over the prone, bleeding, barely conscious Karin and there's a good chance Sakura saw the end of his fight with Danzo. Sasuke demands that Sakura Shoot the Medic First before she joins him. You'd Expect: Since one of Sakura's most noted traits, before being The Load and then Action Girl, was being the Smart Girl, that she would think that something's up with Sasuke and at least not show her back to him. Instead: She does and Sasuke promptly tries to knife her In the Back, prompting a Big Damn Heroes from Kakashi. Worse Still: She almost redeems herself by trying to knife him in the back with a poisoned blade, but chokes at the last second and nearly gets killed. Again. Oh, and Sasuke ended up taking the blade and hits Naruto with it when he pulls a Big Damn Heroes to save her. She came very close to getting Naruto killed through her own ineptitude.
Even more anime filler. While Naruto's travelling to the Land of Lightning, a gigantic eagle kidnaps Guy, who's on the journey as part of Naruto's escort. The rest of the group tracks the eagle to an island, and go ashore to search for Guy. Naruto offers to use Sage Mode's Aura Vision to try and find him. You'd Expect: Yamato and the others to agree with Naruto's suggestion. Instead: Yamato tells Naruto not to do so, claiming that they can't reveal their techniques to the enemy. Never mind that A) they don't know if anyone's around, B) Naruto would quickly be able to discover anyone nearby with Sage Mode, C) all Naruto would be demonstrating with this use of Sage Mode is that he's a sensor, which happens to be quite a well known skill in the ninja world, and D) they're trying to find a member of their group that was kidnapped by a giant bird of prey who could be about to eat him or feed him to its young, as far as they know.
Kabuto has now managed to capture both Naruto and Killer Bee with the rejuvenated Nagato. You'd Expect: Knowing that Itachi is still out there, he'd keep Nagato's Preta Path ability up, as well as create more summons to widen the field of Shared Vision. Thus, when Itachi begins his counter attack he'd be able to easily retort and capture Itachi too. Instead: Instead, he turns off the Preta Path ability thus enabling him to be blind sighted by Itachi in Susanoo, and Naruto and Bee get freed. Adding insult to injury, he uses Nagato to create the Chibaku Tensei and just stands there instead of you know, summoning another bird or one of the Rams or Rhinos in his disposal. He doesn't even keep the Preta Path ability up in the little chance that the Chibaku Tensei gets destroyed, and thus, Nagato gets sealed. Granted, Kabuto probably wasn't aware that the Chibaku Tensei could be stopped or avoided, but he was facing three very crafty ninja; you'd think he'd be more pragmatic.
Naruto is facing Tobi's Jinchuriki Six Paths. They have taken their V2 forms, while he and Bee are standing in front of them. You'd Expect: Naruto to tell Bee to quickly launch a Bijudama before they can attack, or at least enter V2 himself to get back his mobility. And if they got close? Start using his fabled speed and reflexes. Instead: Naruto and Bee stand there, doing nothing as Tobi orders the Six Paths to attack. Bee gets his hand melted slightly, Naruto is hit by three of the Jinchuriki Paths and incapacitated since he forgets about his speed and needs to be saved by Kakashi and Gai.
Kabuto is confronting Itachi and Sasuke. You'd Expect: Him to set up a trap to catch Itachi unawares, knowing what Itachi is capable of. Either a new type of clone, summoning a few of his backup Edo Tensei's, or even hiding under ground since the Sharingan can't see through the earth. Instead: He continues sitting around and lets Itachi break through his barrier. Note, he could have already been in his Sage Mode by then and hit him with his blinding Gatsugei or have the entire earth attack him with Mushi Tensei. No, instead he sits there, bragging on how Edo Tensei can't be stopped and let Sasuke come to back Itachi up.
Sasuke has previously stabbed Karin through the chest and left her for dead, even ordering someone to kill her. You'd Expect: Karin would be justifiably pissed at him and the next time they meet she would try to get revenge, or at the very least refuse to work with him anymore. Instead: She throws a tantrum, beats up Suigetsu for a bit, then immediately falls back in love with Sasuke without anyone telling her to.
Obito, the Big Bad, clearly wants to carry out his Eye of the Moon plan and is currently fighting a one-on-one battle against Kakashi. You'd Expect: That in order to proceed with his plan, Obito would finish Kakashi off as quick as possible by any means necessary. After all, Obito has Wood Release, the Rinnegan, and a Mangekyo Sharingan which allows him to be intangible. Instead: He chooses to fight in the Kamui Dimension where he is unable to use his intangible ability, meaning he's fighting without the advantage of having a Mangekyo Sharingan. In addition, he uses neither his Wood Release or Rinnegan at all. Result: Kakashi handily defeats Obito who ends up with a large hole in his chest. After Madara notices Obito's critical condition, he proceeds to force Obito to use the Rinne Tensei, a jutsu which would kill Obito. This still works out in the end for Obito, though...
Madara thinks he can take out the Bijuu by himself, blind, no eyes, no plan, no back-up, no weapons worth a damn. You'd Expect: Madara to bide his time for Zetsu to return with both of his eyes (especially considering Black Zetsu is currently fighting with his other Rinnegan as opposed to making his way over to his master), so that he can fight to the best of his ability. Instead: He fucking jump rushes all the bijuu without any kind of plan. Because he's a Combat Sadomasochist and actually wants to get carved to ribbons. The Result: Madara becomes a living soccer ball, gains several new holes in his body, and loses his right arm.
Madara spends the first few pages talking to White Zetsu, and takes this chance to summon the Gedou. You'd Expect: Every Bijuu to combine their powers into one large Bijuudama and wipe Madara off the face of the planet, bystanders be damned. Instead: Kurama and Shukaku bicker, with Kurama telling them not to underestimate Madara. Matatabi makes one small remark about how everyone should watch their back. The Result: The Bijuu get their asses handed to them in short order by Madara and are chained by the Mazou, about to be dragged in. And worse, even Naruto and B are chained, and thus, Kurama and Gyuuki are extracted.
Kaguya needs Naruto and/or Sasuke out of the way so they can't seal her. So she drags Sasuke to an alternate dimension that only she can access. You'd Expect: She'd murder the hell out of Sasuke before heading back to finish Naruto off. Instead: She leaves him there and heads back to fight Naruto. The Result:Obito manages to sync Kamui with Kaguya's portals and rescue Sasuke.
Kaguya wants Naruto and/or Sasuke dead. You'd Expect: She'd use her ability to teleport people between dimensions in an instant to teleport them into a lake of lava or into space or something. Put them back at that volcano she first teleported them to. Anything. Instead: While she does make one token attempt, by moving Team 7 over lava (which they easily escaped...somehow), she hasn't actually tried to do anything definitively and immediately lethal to them with this ability, despite their proven inability to resist her teleportation powers. You'd Expect: Her to just...you know...leave. They're already trapped in an alternate dimension, with no way of getting back, so the only thing standing in her way of killing everyone in the world is the Kages, who aren't anywhere near her level. Instead: She tries to fight them. Doesn't go so well for her.
From the fifth movie, Naruto is framed for attempting to assassinate a number of important ninja from various nations, including the Raikage himself. Tsunade knows that Naruto's innocent, but decides to send him to Blood Prison, due to the fact that there's a MacGuffin there that Konoha wants destroyed. You'd Expect: Tsunade to assure Naruto that she knows that he's not guilty, and give him a mission to play along with the accusations, and go to Blood Prison to destroy the MacGuffin. It's not like he'll mind such a mission, given his patriotism. Instead: She just has him restrained, and forcibly taken to the prison. As a result, Naruto believes that someone's trying to get him out of Konoha to weaken it, and spends more time trying to break out of the prison (and getting shut in solitary confinement for it) than looking for the MacGuffin, making Tsunade's actions near-pointless. That, and her actions would have probably convinced someone other than Naruto to defect, on the basis that she'd apparently sold him out. Worse: At one point, Naruto nearly dies trying to escape Blood Prison, and is only saved due to the actions of a third party who was also unaware of the mission. Tsunade's apparent refusal to tell Naruto the truth nearly lost them the Nine-Tails, a rather handy deterrent against the other ninja villages.
After a battle with the Akatsuki, Naruto has witnessed the parents of his classmates offering to recommend to Tsunade that they be promoted to Jonin. Rather understandably, he goes to ask Iruka, the closest thing he has to a parent, to ask him if he can do the same for him. You'd Expect: Iruka to give something along the lines of one of the following responses, depending on whether or not he thinks Naruto's worthy of the position: Response 1: "I would, but you'd need to become a chunin first, before you could become a jonin. Sorry Naruto, that's just how the system works here." Response 2: "Sorry Naruto, but you're still too *insert flaw here*, and because of that, I can't recommend you. But if you can sort that flaw out, I'll consider it." Instead:(quite callously) "No, I won't. You have to become a chunin first. You may have saved the village from Pain, but we're not going to give you special treatment." It comes off as very mean spirited of him, since Naruto hasn't done anything to justify Iruka being angry at him lately, nor did he ask for any special treatment, just a letter of recommendation which the rest of the Konoha 11 are apparently all getting. It's an idiot moment because Naruto was already feeling depressed. Even worse since one might expect that saving the village from an opponent that rather effortlessly destroyed it would earn special treatment. Or at least a promotion to chunin.
Shortly after the above scene, Sakura has dragged Naruto off so that she can vent to him about how annoying she finds her parents, and that she wishes they didn't even exist. Soon afterwards, Sasuke gets involved in the conversation. You'd Expect: Sakura to remember that Sasuke took the death of HIS parents very badly, at one point showing clear disgust at her for thinking that not having them would be a good thing, as well as running away from the village solely so that he could become strong enough to kill the guy responsible for their deaths. In case it's not clear, he really misses them. Instead: Sakura seems to think that Sasuke would understand her desire to not have parents. Not making this up. Depending on whether or not you consider the Naruto movies to be canon, at this point in the series, you could probably consider Sakura a hypocrite whenever she calls Naruto out for idiocy.
Tobi can teleport wherever he wants on a whim without anyone having any way of actually knowing he's done so until he's there, and them similarly having no actual way of stopping him. You'd Expect: Tobi to appear whenever Naruto leaves the village, ever, and/or is either alone or with only a few people who aren't expecting immediate danger, and try and capture him. Hell, Naruto's childhood would have been a perfect time to try it (remember, Naruto was alone most of his life, Iruka and others acknowledging him is a major part of his story arc). Then he can either extract the Kyuubi to use as a weapon, or hold him until the Kyuubi is necessary. Granted, he might not have known what happened to the Kyuubi after his last intrusion into Konoha, but he could have easily infiltrated the village and kept his ears out for any information on the fox. Instead: Tobi just leaves Naruto alone for 13 years instead of actually trying to capture him. Then sends Itachi and Kisame to try once, then ignores him for 3+ years, particularly while he's out in the world with only Jiraiya to protect him. Addendum: Obviously this applies to the other 8 Jinchuriki as well, making Akatsuki ultimately totally superfluous in nearly every possible way, aside from unsealing the tailed beasts.
Naruto is asked twice in the series whether Sakura is his girlfriend. You'd Expect: Him to answer truthfully; she isn't (at this point in the story). Instead:He says that she is. Sakura reacts violently on both occasions. Even if she wasn't in earshot, lying about your status with someone is generally not good for your relationship with them.
Also relating to Naruto and Sakura, Naruto frequently asks Sakura out on dates. And Sakura says no to him time and time again. You'd Expect: Naruto to get the message that Sakura isn't interested in him that way, and move on. Or, try and find out WHY she won't go out with him. Instead: He continues to ask her, and she continues to turn him down.
Shortly after his death, and confirmed by multiple sources, it is revealed that Itachi was a spy for Konoha while in the Akatsuki. You'd Expect: Itachi, at some point after he left Konoha, to have set up a steady flow of information to his village on the Akasuki's activites, such as the details of extracting the bijuu, his "teammates" powers and abilities, etc. in order to give as much of an advantage to Konoha. Instead: Itachi actively helps the Akatsuki extract the bijuu, never exchanges info despite his genjutsu abilities, and the heroes were in more dire straights when the bijuu count eventually dropped down to two still in their possession.