So, it turns out that taking on a heavily-armed unit of former Russian Commandos armed only with an ax isn't that good of an idea and Infant Immortality doesn't exist. I'm looking at you, Hansel.
For that matter, the rank-and-file thugs of the series attempting to take on Special Forces-quality groups like Hotel Russia or Gray Fox usually ends badly for them. Even when Roberta, who has been seen effortlessly wiping out huge groups of Roanapur's criminal element, takes on the Gray Fox unit, she manages to kill most of them but very nearly dies in the process, losing an eye and a couple of limbs.
While Blitz Stanford, an enormous neo-Nazi is extolling the virtues of his enormous Luger, Revy takes the opportunity to reload and promptly shoot him.
In one arc Revy sees a group of kids playing cops and robbers. Revy then has one of the kids use a toy gun on her just so she can show them just what really happens to a person when they die after being shot. Not as overly dramatic as they pretend it to be.
Revy and Roberta's fist fight isn't glorious nor intended for fanservice. It was as brutal as you'd expect from two trained killers.
On that same note, expect some bruises and swelling in this series when people get punched in the face, not just standard anime scratches. Even when Revy punched Rock in the face during a moment laden with sexual tension, his face swelled up and bruised. Several episodes later, the bruise is still there.
In Black Cat, Train is falling off a building and Rinslet jumps off to catch him, ending when Rinslet comes to a sudden stop at the end of the rope — and actually does tendon damage to her arm. Turns out inertia matters after all...
In the first chapter/episode, Kouji did not think that Falling into the Cockpit of a huge, dangerous war machine was a bad idea. Needless to say, it was. He trashed half the city because he kept punching random buttons while he tried to figure out how to make it work. Said trashing included playing baseball with cars -with the driver inside-, and smashing a school to pieces. When Sayaka showed up, Kouji began to cry out of relief.
The anime has Kouji come out a bit better, but not much. He nearly gets his head cut off by the cockpit glass shield, blew up his grandfather's manor and remodeled part of the landscape, and almost stomped his little brother Shiro flat. And this was after Shiro had warned Kouji not to try anything.
No Endor Holocaust gets deconstructed several times. It turns out that, when two Humongous Mecha duel in a city, there's a lot of damage. Buildings crumble down and catch fire, lots of people die, and the survivors blame the heroes for most of the destruction.
Kouji and Sayaka were a Battle Couple whose Belligerent Sexual Tension made them highly ineffectual in battle. The Dragon, Baron Ashura, exploited this in an episode where Kouji got badly injured because he got a serious fight with Sayaka, and she refused to fight alongside him.
In episode 48 of the anime, Boss cajoles/threatens Professor Yumi's assistants into building him a giant robot made with a box of scraps. He wanted a mecha that was more powerful than Mazinger-Z itself. What he got instead was a Deconstruction of the Humongous Mecha: Boss Borot is goofy-looking, slow, clumsy, heavy, breaks easily, takes ages to stand up if it falls over, and lacks anything remotely useful for a weapon. The scene includes Boss asking for all Mazinger's weapons, one after another, and Morimori explaining every time that they would not work and Mazinger can only get away with it because it is powered by Phlebotinum and Made of Indestructium (that Boss' robot is not). When he asks for a Rocket Punch, Morimori explains that anything like what Boss wants would shatter on impact. Because, you know, it's a missile.
An episode of Cromartie High School has Mechazawa destroyed and rebuilt as a Cool Bike, complete with missile launchers. Kamiyama uses Mechazawa to save a young woman who is being harassed by some thugs, only to immediately be arrested for property damage. Kamiyama attempts the same thing a few episodes later and purposefully tries to avoid any Collateral Damage, but still ends up being arrested on the grounds that he doesn't have a motorcycle license.
One of the main reasons Minato Namikaze was so deadly; due to his speed he made speech NOT a free action.
Konan prepares to give a rant on how Naruto is the bridge of peace in the middle of a battle. Tobi doesn't even let her finish her sentence.
A relatively subtle example shows up with Sakura and Naruto's contrasting shortcomings early on. Sakura gets good grades in class, and is the only one able to actually answer the seemingly impossible questions in the first stage of the Chunin Exam, and ends up looking down on Naruto, last in his grade. But in the Forest of Death, Sakura's lesser combat ability proves a problem when Naruto and Sasuke are incapacitated. Similarly, while Naruto's very good at fighting despite being Book Dumb, some of the things he failed to learn in the academy come back to haunt him in his training; he regrets not paying more attention in class when trying to learn how to focus his chakra for his Rasengan training.
Early in the series, Naruto is poisoned in battle. The poison is spreading slowly from his hand and Sakura surmises that the best course to take would be to use a surgical incision to drain the poisoned blood. Since the team would have to go back to the village and abandon their mission to do that properly Naruto violently stabshishand with a kunai to quickly drain the blood (and also as a dramatic gesture in a vow to never again be paralyzed with fear like he was during the fight)... and than goes into a panic attack when Kakashi points out that he's probably gonna bleed to death from a wound like that. Fortunately the tailed beast within him easily healed the wound.
Post-Pain Arc, Naruto has been running himself ragged with him unable to talk to his adopted "grandmother" Tsunade due to her coma in the ensuing invasion. He learns Sasuke has become a criminal and attacked a fellow Jinchuriki for Akatsuki. He learns that his friends, even Sakura, have given up on bringing Sasuke back to Konoha. Then when he's told there will be War on top of everything... he can't take it anymore and passes out. A realistic depiction of a Determinator when pushed to the limit.
What killed (or crippled him for the rest of his life) the legendary Madara Uchiha during his battle with Hashirama? An epic ninjutsu clash? Nope... a stab through the back.
Similarly, After he was revived, Madara managed to become fully human, while this gave him full autonomy over his rinnegan and made him a deity in power, a stab to the back from Zetsu kills him once more, allowing the Bigger Bad to reincarnate from his body.
Zoro suffers grave injuries that put his life in danger — as usual. But, unlike the other times where he has an Unexplained Recovery and the injuries are usually never mentioned again, one arc later Zoro tries fighting and his wounds cause him to be temporarily paralyzed. And then two arcs later, even after resting and being treated (by Perona, believe it or not), his wounds re-open when he tries to fight and move, resulting in him getting his ass kicked by Apes. He muscles through them some (small) time later — after they copied his skills and called out the toughest one of them.
After being defeated by Crocodile for the second time, Luffy rushes to confront him again only to pass out from blood lost a few minutes later. He does recover, more-or-less, after a few minutes of sleep.
Luffy put everything he had in defeating Lucci to the point where he couldn't move afterwards. Unlike the other arcs before, however, Luffy and his crew are still in danger despite all the most powerful fighters being defeated and the marines nearly kill Luffy became he is too weak to move when they aim their cannons at him.
Characters having to fight through grievous injuries is also brought up in the Arlong arc, where Zoro is at a disadvantage in his fight against Hachi due to a massive chest wound inflicted on him by Mihawk that was very amateurishly patched up. Through he does eventually win the fight, Hachi attempts to attack Sanji later on and almost succeeds in taking him out, only for his wounds to open up again at the last second, taking him out of the fight before he can do anything.
Luffy himself once tried fighting a man who could produce and attack with deadly corrosive poison. Seeing as how only Mooks had been poisoned by Magellan (the man in question) at this point, the audience and Luffy himself thought he stood a chance from the moment Luffy launches a Jet Bazooka that actually DROPS the hulking Magellan... but no. Touching him with that attack and many more poisons launched at him nearly kills Luffy within just 2 measly episodes of starting the fight.
At Marineford, Luffy is willing to give his life to save his brother. Too bad for him that he is one of the weaker fighters in the war on top of the injuries he gained from going to Impel Down. He is mercilessly knocked around by the marines and the Warlords.
Kizaru: You have to have more than just courage. Willpower alone means nothing without strength. Strawhat, without enough strength, you cannot save anyone no matter how hard you try.
Giants Dorry and Broggy had been fighting for almost 100 years with their weapons and fists: it turns out that, after 100+ years, even with constant maintenance, weapons will eventually break. This was a rather joyful use of this trope, however, as everyone had thought Dorry had been killed.
At the start of the Fishman Island Arc, Sanji (Who had spent the last two years on an island full of only Gonk transvestites) suffers a nosebleed every time he sees a genuine woman. While this is comedic in every other anime (and every other time in this one too), the frequency and severity of the nosebleeds caused near-fatal hemorrhaging at one point, requiring some immediate blood transfusions. Furthermore, Sanji has a particular blood-type and while fishman and humans have the same blood, a law forbade the transfusions due to the long history. A more minute example occurred at the end of the arc when Jimbe offered to give blood to Luffy, who saved the day. When pointed out about the law, he reminds the people he is still a pirate.
Checkmate from Ultimate Muscle has a similar problem. While injuries that don't affect his body mechanically don't slow him down, he has an unfortunate tendency to collapse from his wounds at the worst possible moment because he never knows when he's too hurt to keep fighting.
It shows the consequences of having young children with no military background piloting Humongous Mecha. By the end of the show, two of the young pilots suffer severe psychological breakdowns, one ends up crippled, and another is violently killed while pulling a Heroic Sacrifice.
The aftermath of repeated battles within city limits is that, by the end of the show, Tokyo-3 has to be evacuated due to the sheer amount of property damage.
The fight with Ramiel (a gigantic Crystal Angel) ends with them blowing a hole in it, and leaving its corpse on the city. For the next three episodes, cranes and other crews can be seen disassembling the corpse.
Long before Evangelion, Zambot3 showed how kids being pilots of a Humongous Mecha can actually be psychologically straining, and how immaturity can lead to deaths. Kill 'em All indeed. Also, cities do not get magically repaired after getting smashed down during a battle between giant robots, and often the cast has to fight on the ruins of a city destroyed in an earlier battle.
The Demon World Tournament subverts the usual formula. The main characters and villains aren't placed on opposite sides of the bracket (in stark contrast to this happening with Yusuke and Rando in Genkai's tournament, and Team Urameshi and Team Toguro in the Dark Tournament) and end up facing each other in the quarter finals. The main villain defeats the main character, but expends so much energy doing so that he loses to some no-name in the next round, allowing a minor character to come from behind to take the win.
In a minor part of the Dark Tournament arc, the giant robot that can't feel pain can't tell that it was actually damaged... until it's under the opponent's control already.
In the first episode, Kenshin dodges Kaoru's attack and lands on some wooden crates that break apart when he lands because crates aren't built to hold a person jumping on them.
Kaoru fights Gohei, who's several times her size and using a katana, with a bokken. She's quickly disarmed and nearly killed. Kenshin lampshades this.
Kenshin: It's rather reckless to use a wooden sword against a real one.
Sanosuke's Zanboto is so ridiculously big and heavy that Sanosuke can only swing it in two, easy to predict ways. Its size also makes it impossible to maintain its edge, so it has become dull.
In an early arc, a group of elite warriors are done in by a gatling gun.
Gein's super Iwanbo gets destroyed because he couldn't tell it was damaged.
Sanosuke's ultimate technique, which involves putting so much force into a punch that it tends to fracture the bones in his own hand. His doctor is not amused.
Kyoto Arc's Big Bad Shishio Makoto immolated himself because he couldn't sweat and he overheated. While the actual Man on Fire part is an exaggeration, the overheating is a very real and potentially deadly consequence of anhidrosis.
Kenshin's smaller build means that, once he learns the Hiten Mitsurugi Ryu ultimate technique, he accumulates minor muscle damage. By the end of the series he's told that he won't even be able to wield a sword in five or so years.
Saito Hajime seems to evoke this trope constantly. His fights against Kenshin are very dirty, and he's willing to use any fighting technique he can get his hands on. He also forces Kenshin to revert to his old fighting style as an assassin, showing he's been hiding back for quite some time. Finally, Saito has one ultimate technique, with multiple ways of launching and aiming it. In the end though, he's just setting up a head thrust and it turns out that is the one place Shishio Makoto fortified against attack.
In Loveless, the Zeroes are a series of Artificial Humanswithout pain receptors with the idea that this would make them unstoppable in a fight. Soubi figures out how to exploit this by lowering the temperature of the area they're fighting in until the two develop dangerous hypothermia with no way for their bodies to counteract it.
Early in Outlaw Star, the crew blast their way out of a spaceport to evade space pirates, presumably causing hundreds of thousands of wongs in damage. Towards the end of the series, the crew returns and Gene is immediately arrested and thrown in jail for property damage and other laws he broke, and only gets out at all because the traffic controller had been found to be taking bribes.
In The World God Only Knows, Keima notices that unlike in a game, when an idol confesses their love to you, other people are generally not happy. In fact, they're pissed.
Freezing features beautiful girls who attack each other with sharp weapons. When their clothes get ripped apart, so do their bodies.
Played straight earlier on, when after dramatically ripping up their drafts of Money and Intelligence and throwing them into a river, Mashiro and Takagi run away lest they be caught for littering.
Also played straight earlier on in which after Takagi punches Ishizawa for insulting Mashiro, he gets suspended.
Toward the end, once Mashiro and Azuki's relationship comes to light, very few people are happy to hear it, there is a large In-UniverseInternet Backdraft, and this makes it more difficult for Azuki to get the lead role, since people think Mashiro might be favoring her.
In Gekkan Shoujo Nozaki-kun, Nozaki offers to give Chiyo a ride on his bike. Chiyo assumes this will be an intensely romantic gesture, until Nozaki reveals that they'll be riding on a tandem bicycle. Turns out that the common romcom trope of having two people riding together on a single-person bike is technically illegal under Japanese traffic laws.
In Azumanga Daioh, Osaka, of all people, pulls this when she wonders what Chiyo would do if she was kidnapped. Chiyo suggests that Tadakichi-san could come to her rescue, and Osaka mimes shooting him. This leads to this exchange:
Chiyo: So what should I do? Osaka: If this was a TV show, you'd use your genius brain to think up somethin'... and fight back against incredible odds... Osaka: ... and get killed.
An episode in Soul Eater where Death the Kid first starts attending the DWMA, Black Star climbs up near the top of the academy building to deliver a Badass Boast to Kid... who's standing near the front entrance and can't hear a word he's saying because he's so far away.
Additionally, it is bluntly stated that Iono simply does not have time for all of those concubines, especially since she still does have to rule her country, and still likes going out to meet more women. So there is loneliness, infidelity, and infighting among the harem.
Mobile Suit Gundam 0080: War in the Pocket has a boy and his friends get excited about the Federation/Zeon war and treat it as a game. Then the boy befriends a Zeon mobile suit pilot and experiences it first-hand. For that matter, the Zeon pilot in question is a rookie looking to redeem himself after an embarrassing first battle. He's shown to be a good guy with even a bit of a heroic streak in him, and in the end faces the Gundam not out of orders from Zeon superiors, but in a selfless attempt to prevent a massacre. He dies fighting the Gundam despite his best efforts, as the Gundam is a superior machine and he is still a rookie pilot. Moreover, the story goes to lengths to show that the massacre he was trying to prevent had already been stopped without his knowledge, so his tragic death was entirely meaningless.
The show plays with this trope from time to time, when less badass pilots find themselves unable to pilot even the prototypes of the Getters due to the stresses of the G-forces.
Getter Robo Armageddon has a moment where the heroes are in the title mecha with Ganymede, the biggest of Jupiter's moons looming front of them. They unleash the mech's most powerful attack: Stoner Sunshine, on it. The attack does absolutely nothing to it.
Gunslinger Girl: After all the fighting, the dying, and the drama, the terrorist organization is eventually brought down by diplomatic means, the Social Welfare Agency is closed down by the government since they need a convenient scapegoat, a political shitstorm is raised over their use of little girls in their experiments, and Elizabeta/Petrushka does, in fact, die from cancer (replacing her limbs only allowed her to fight, it didn't cure her, after all).
The Excel Saga manga likes to delve into this often, compared to its far wackier anime counterpart (the tagline for the manga is even "What would happen if you tried to act like an anime character in real life?") One major example is Ropponmatsu I, a Do-Anything Robot stuffed so full of gadgets that her body is extremely heavy. When her creator is asked if he could create a body with the versatility of Ropponmatsu I and the weight of Ropponmatsu II (who weighs about as much as a normal human but lacks all the gadgets), he blows off the idea as ridiculous.
20th Century Boys has a scene where a skilled roboticist is brought before the Friends to build a doomsday robot. The Friends start talking about how all the classic Humongous Mecha tropes they want the robot to follow, only for the roboticist to explain in detail how something like that is impossible to replicate in real life (including citing the Square/Cube Law and explaining that there'd be so much movement just from walking that trying to pilot it from inside would cause motion sickness.) In the end, the robot that gets made is really just two robot legs on tank treads attached to a giant balloon.
When Goku gets injured in his fight with Vegeta, there are no Senzu beans available. He recovers at an impressive speed considering his injuries, but he spends a month recovering in the hospital before there are more Senzu beans. Played up even more in a filler arc during this, where Goku escapes the hospital and attempts to resume his training but because he hasn't properly recovered yet winds up injuring himself even more and immediately gets re-hospitalized.
Played with this at one point. Videl, fresh from learning how to harness her Ki and fly, is forced to sit a mission out when she's unable to see while flying due to traveling at high speeds without any form of eye protection.
Before his sacrifice against Majin Buu, Vegeta, being somewhat aware that in Dragon Ball Death Equals Redemption optimistically asks Piccolo whether he would see Goku in the Other World. Piccolo then bluntly tells his (in so many words) "No. Unlike Goku, you've been a selfish, evil asshole for most of your life and this one selfless will not make up for it. You're going to Hell when you die." And he did. Thankfully he got a second chance and was brought back to life when the Universe was on the brink of extinction.
Being a Super Saiyan may seem cool, but if you can't control the power that comes with it, it can essentially turn into Blessed with Suck as the effect it can have on your mind and body can bite in the ass in the worst ways. With every new Super Saiyan transformation you either turn into a bloodthirsty sociopath hell bent on making your worst enemy suffer, significantly grow in muscle mass to the point where you practically can't throw a punch and move very slowly to the point at which you're defenseless, bring near total devastation to the world or burn through all of your ki in a matter of minutes and leave you powerless. Even if you master the Super Saiyan transformation doing mundane tasks can still be an issue. Case in point where in one scene, which laps over with Hilarity Ensues, where Goku and Gohan couldn't even hold glass cups without breaking them, even when holding them delicately. They then proceed to unintentionally casually destroy the entire kitchen in Goku's house just because they were in it!
Considering how strong the Z-Fighters are any mundane task is difficult. Naturally because of Goku's Super Strength even the lightest tap could send somebody hundreds flying of feet into the air... which was the case when Goku playfully slapped Chi Chi on the back and sent her flying out of the house, crashing through a tree and crashing into a rock. It's a good thing she's Made of Iron and only suffered a few bruises and cuts.
During Goku's fight with Ginyu Force member Recoome during the Frieza Saga, Recoome realized Goku was a real challenge and brags about showing him his special move, the "Recoome Ultra Fighting Bomber". When he goes into his elaborate windup to prepare the attack, Goku just punches him in the stomach, stopping the move mid action. Lampshaded by Goku, who points out how Recoome was so open to attack, he couldn't help himself.
Cell announcing that he will essentially destroy the world if nobody can defeat him at the Cell Games in 10 days on worldwide television gets the sort of reaction you would expect... the entire world is thrown into chaos as all of humanity panics in terror at the fact that the world is gonna end in 10 days. Thousands of people try to evacuate from cities worldwide and the world's Army is immediately sent to try and destroy Cell, only for Cell to destroy all of the army without breaking a sweat. And of course, this was the sort of reaction Cell was hoping for!
Gohan tried to take on the Androids on his own after just recently nearly dying and losing an arm. He's overwhelmed by the Androids and dies very horribly.
One of the supposed safe haven towns left on Earth has an amusement park that is constantly open and considering how loud amusement parks are it doesn't take long for the Androids to find and destroy it along with all of its inhabitants.
When Android 18 goes clothes shopping and after she finishes raiding the store of all the clothes she wanted with the "consent" of the store owner and employees, Android 17 destroys the store and employees inside of it. What, did you actually think they would let them live? Remember, they're programmed to hate all humans, no exceptions.
Trunks attempts at bum-rushing the Androids on his own only results in him getting his ass kicked so bad he ends up in the hospital for days in critical condition.
Fullmetal Alchemist has four major ones with Ed's automail. 1) Anytime it gets significantly damaged, he has to go back to Winry because he doesn't know how to fix it, especially if it's his other arm. 2) A version that was 80% lighter was also far more fragile. 3) When he traveled up north to Briggs, he nearly dies of frostbite because his two metal limbs conduct heat away from his living flesh. He also had to have it adjusted whenever he grew, as his real leg would end up taller than his automail leg. Fortunately (and unfortunately from his perspective due to him despising his short stature) this happens very rarely in the series proper. 4) Ed can't stand the desert since his automail gets hot enough to literally cook with.
In Girls und Panzer, the last team to join the Oarai tank crew is composed of three girls who have experience playing a tank game online. They learn the hard way that the tank doesn't operate as simply as the ones they're used to controlling in the game do, and end up accidentally reversing into the path of a shot that would have struck their team's flag tank.
The Hentai game turned Anime, School Days, deconstructs the Harem Anime genre by showing what could realistically happen when a male gains the attention of many females. It also shows what can realistically happen during a serious love triangle as well. None of it is good.
Eren is a huge smack in the face for the standard Shonen hero tropes. Full of Hot-Blooded rhetoric and a passion for vengeance, he rushes headlong into action without any consideration for the abilities of himself, his allies or his enemies, and constantly puts himself and others at risk.
Just because mankind is facing extinction doesn't mean it will magically forget all its interpersonal and political issues and become fearless heroes. Lampshaded by Eren, of all people, who remarks that before the Titans appeared humans wrote a lot of stories about uniting in the face of a greater enemy, and he found them ridiculous.
The Survey Corps wield absurdly sharp blades to fight the titans, but also have to carry roughly a dozen of them because the same properties that make them so sharp also make them very fragile and vulnerable to dulling.
The Titans are terrifying, and inflict horrible deaths on their victims, so it's all but impossible to avoid being frightened of them. It's nicely shown near the beginning of the story, in which Hannes, faced with the choice of saving Eren and Mikasa while leaving Carla behind, or staying and letting the Titan eat them, considers killing the Titan so he can save all three, but panics at the last minute and decides to escape with the kids. Carla tries to Face Death with Dignity, content with the knowledge that her children will be safe, but breaks down and can only cover her mouth to prevent the others from hearing her screams.
This show also shows why it's not a good idea to have a Living Emotional Crutch and the dangers of Undying Loyalty; when Mikasa believes Eren has been killed, she has a mental breakdown, which causes her to recklessly throw both herself and her squad at the Titans, resulting in many of the soldiers under her command being killed. Similarly, when Eren is kidnapped by the Female Titan, Mikasa loses herself in anger and tries to kill it—which, if not for Levi, would have gotten herself killed and allowed the Female Titan to escape. Furthermore, Levi's action to save Mikasa, causes an injury putting the best soldier they had against the Titans out of commission.
Sailor Moon: A note to Usagi Tsukino: when you're sentenced to Standing in the Hall as much as you're implied to have been, your grades will suffer. Didn't Haruna Sakurada point that out to you that time you got a 30 on your test?
Usagi's panicking in battle is pretty much what would happen if you throw a teenage girl into life or death fights.
Also, being the queen of a Utopia and the savior of the world doesn't help a whit if you're Book Dumb and lazy; far in the future, Usagi still writes using hiragana (when most kids would be learning how to write kanji in elementary school).
Cardcaptor Sakura: Meiling is strong enough to smash some park penguins with her fists, but it left her hands terribly injured doing so.
The first episode of Servant × Service ends with Lucy chasing Hasebe around the office after getting tired of his inappropriate remarks. The Stinger then shows them being lectured by a supervisor about how violence in the workplace will not be tolerated.
In Bokurano, similar to other deconstructions of Humongous Mecha above, the heroes cause a large amount of collateral damage in their fights (thousands of people die almost every time), and end up getting blamed for it, to the point at which some people try to kill them, and essentially succeed on Machi in the manga. It's also shown as a less than good idea to give a giant mecha that is more powerful than any Earth military technology to twelve year olds, some of whom are unstable or have ulterior motives, especially when they know they're going to die after they pilot. To make matters worse, according to Koyemshi in the manga, the main characters' group actually turned out relatively well compared to the one he and Kokopelli were in.
From the same author as Bokurano, Narutaru. A brutal Deconstruction of the Mons genre that explores what would really happen if a bunch of teenagers got superpowered pets. A lot of people die, the military gets called in, and things only get worse. Ultimately, there's very little mundane forces can do to someone wielding the godlike power of a Shadow Dragon. For a more specific example, the first villain in the series is an angry teenage boy who thinks it'd be awesome to kill a few billion people and send things back to the stone age as a form of Social Darwinism. And he can, because he has a Shadow Dragon.
It also shows what happens when a magic dependent society and military runs into opponents who possess Anti-Magic strong enough that it simply can't be overpowered and they have to resort to prototype weapon system that convert their magic into mass weapon projectiles just to hurt and slow their enemies down. It also shows why relying on largely untested prototype weapons is dangerous in and of itself.
Two recurring villains in the final arc of The Daughter of Twenty Faces are a pair of Creepy TwinSuper Soldiers who Feel No Pain. During the penultimate episode, Kozomi and Ken manage to defeat them by tricking them into repeatedly pummeling steel support structures, which eventually causes severe joint and muscle damage. Nozomi notes that the inability to feel pain meant the twins were unable to realize they were destroying their bodies until it was too late.
In an early episode of Code Geass, Lelouch calls for the support of a group of terrorists/freedom fighters to fight back against Britannia. His first time trying that, against an inept commander, it worked well. The second time was against an enemy that actually knew what they were doing. Sure enough, Lelouch's untrained and undisciplined allies lost their heads and tried to surrender at the first sign of trouble.
Rolo's powers in the series are apparently stopping time, but later on its revealed that he's really only putting your brain and his own heart on pause so it looks like he stopped time. The reason he never uses this for longer than a few seconds is because he's putting himself into cardiac arrest and near the end of the series when he uses it for an extended period of time it ends up killing him.
In one memorable chapter of Tokyo ESP, because Rinka never hid her true identity her house gets burned down by a criminal and several terrorists invade her school and give her a No-Holds-Barred Beatdown to the point that she actually died for a few minutes.
Jormungand: Koko's Badass Crew may be good at what they do, but even they can't prevail against elite special forces, namely when the US sends the Navy SEALs of Night Nine against them. Despite their efforts they're firmly on the backfoot, don't manage to kill a single one of the foe and even Koko's assistance barely lets them etch out a withdrawal. Very stark because they are usually Showy Invincible Heroes.
In Fruits Basket, neglect and emotional abuse leave characters nervous wrecks who are insecure, prone to lashing out, have little to no self esteem, and have difficulty forming relationships with others. Also, Akito constantly being told by her father that she's special because she's destined to be loved as the head of the Zodiac is one contributing factor to her being such a mess as a teenager. Her being The Chosen One really didn't make her a better person.
In Bitter Virgin, Hinako's fear of men is not magically cured by her falling in love with Daisuke. At best, she realizes that she feels comfortable with him alone. The ending also heavily implies that the relationship between the two won't last. No matter which way it goes though, it's clear that both will have to fight to make things work with Hinako's emotional baggage.
When Daisuke's crazy Stalker with a Crush tries to frame him for raping her, Hinako immediately knows that a rape victim wouldn't be acting the way she is and, put together with Daisuke's previous Nice Guy behavior, comes to the correct conclusion that the girl is just lying.
Early Bleach has Ichigo frequently carelessly leaving his physical body lying around when he leaves it to go into Soul Reaper mode. The first movie, Memories of Nobody, brings up the consequences of this when Ichigo returns to find a small crowd gathered around his body and paramedics trying to revive him.
At one point in Cowboy Bebop, Spike tries to use his badass flamethrower as a lighter...and promptly incinerates his whole cigarette to the butt.
In the Area 88 manga, Mario forgets that elaborate aerial maneuvers can be extremely punishing on a pilot's body. While executing an outer loop, he's overwhelmed by the G-force and crashes to his death.
In the Monster Rancher anime, Genki's excitement at being pulled into the monster world doesn't go over well with Holly and Suezo when he acts dismissive of the very real threat Moo poses. He gets a further wake-up call upon seeing the effects of Moo's actions firsthand.
Genki may be great at rollerblading, but they don't make very good shoes for traveling over unpaved roads and rough terrain. Fortunately, a kindly old couple provides him with some more appropriate footwear, along with a cloak.
In the last arc in Great Teacher Onizuka it turns out that all those injuries that Onizuka has received over the course of the series and its prequel actually have been hurting him a lot more seriously than anyone previously imagined. The numerous head and body trauma he's attained have resulted in him developing a brain aneurysm that winds up nearly killing him.
Played for Laughs in Sakamoto Desu Ga. Sakamoto uses the Rule of Cool so skillfully, that people come to expect impossible stunts from him... which, every now and then, he subverts by actually doing something perfectly sensible that only looked like a weird stunt because of his audience's expectations.
With his street fighting experience and Anti-Magic, Touma Kamijou can handily defeat street thugs and people who rely exclusively on their powers. Against people who actually know how to fight, and people who are way stronger and faster than him, he gets his ass kicked, a lot. Also, despite his Healing Factor, he gets hospitalized a lot, since it tends to work too slow to matter in a fight.
When enemies pull out guns, Touma is forced to run, hide, and use trickery to win.
Since Touma spends all his time saving the world, he has poor school attendance and does poorly on assignments and tests.
Mikoto Misaka trying to go One-Man Army on the clone facilities without resting or telling anyone what she is doing ends up with her running herself ragged and almost getting killed by Frenda and Mugino. Also, the company outsources, so no matter how many facilities she destroys, it doesn't affect the project.
Accelerator was so dependent on his powers that in situations where he couldn't use them, he gets his ass kicked and almost gets killed, until he starts using guns and fighting smarter.
Misaki Shokuhou was so dependent on her mental powers doing all the work for her that she's out of shape and can't jog a short distance without getting out of breath. She also needs people to save her from enemies who are immune to her powers.
Othinus was so arrogant about her immortality and invulnerability that she wore a skimpy outfit so show off that she can't be harmed. Then she loses her powers, almost freezes to death, and has to rely on Touma to keep her alive from all the people who want her dead. Without her powers, she can't do feats that she once considered child's play, like jumping onto a moving truck.
Acqua of the Back's sword Ascalon is 3.5 meters long and weighs 441 pounds. He's forced to leave it behind when he loses his powers, since he needed his Super Strength just to pick it up.
Detective Conan kicks off it's entire plot with a Reality Ensues moment: We're introduced to Shinichi Kudo (Jimmy Kudo in English) a hotshot modern day Sherlock Holmes. He's shown solving a couple of complex murders to establish his character, then he goes off and spies on a couple of suspicious guys in black trenchcoats...only to get nailed in the back of the head and force-fed poison. Hotshot ace detective or no, going off to follow a couple of thugs without any backup (not even, say, the trained martial artist currently accompanying you) was a stupid plan, Shinichi.
Crops up from time to time in The Big O. Notably Beck's Combining Mecha, shown to be extremely extravagant and flashy in comparison to the slower and bulkier title mech. However Big O is a solidly built war-machine, and manages to blow apart the Megazord-esque robot in the span of a few seconds with just a few shots from it's sidearm.
Big Fau's rocket punches in the finale are casually caught by Big O mid-flight, causing them to detonate and leaving Big Fau relatively harmless.
At the end of Nerima Daikon Brothers, the titular characters are being badly beaten by the corrupt Japanese government officials. The show's resident panda cub, up till now solely a participant in various gags, calls in several hundred of his friends in a Big Damn Heroes moment, to create an army of cute, cuddly panda cubs to fight the forces of evil. Aaaannnd...they fight about as well as you'd expect panda cubs to fight, losing the battle in seconds in a horrible curb stop battle.
Love Hina: During the manga's Christmas Special, Motoko is groped by a chikan on a train, and proceeds to beat him to the bloody pulp. For once in the series, Double Standard: Abuse, Female on Male is averted, and Motoko finds herself in hot water with the cops as a result.