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 time to reload before promptly shooting him.
In one arc Revy sees a group of kids playing cops and robbers. Revy sees one of the kids 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.
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.
In the Persona video games, the underage protagonists often use various armaments (including firearms) to battle their enemies. Persona 4: The Animation pokes fun at this recurring trope by featuring a scene where Yosuke brandishes a Samurai sword in public, only to be quickly arrested along with the protagonist by nearby police officers, who are already on high alert because there's a killer on the loose.
An episode of Cromartie High School has Mechazawa destroyed and rebuilt as a Cool Bike, complete with missile launchers. Kamaiyama 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 dramtic 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. 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.
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.
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.
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.
Even before Evangelion, Zambot3 shows 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.
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 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.
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.
Dragon Ball Z plays with this at one point. Videl, fresh from learning how to harness her chi 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.
Fullmetal Alchemist has three 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.
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.
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?
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.
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.
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.