In Hajime no Ippo it's shown during his fight with Takamura that Brian Hawk was nearly mugged in the streets of New York. Of course, it wasn't successful as Hawk proceeded to beat the mugger nearly to death with his bare hands.
The guy who wanted to rob a karaoke bar in Tower of God really has bad luck. First of all, he picked the bar where the Action Girl who easily kicked the ass of every strong regular in the first season works. He also thought impersonating a recent infamous criminal for extra intimidation was a good idea, but unfortunately, that girl is the criminal's companion. She provokes him with her snarking, he attacks and he goes down. Felled by the hand of said criminal who happened to walk in at that exact moment.
A bunch of slavers to try and intimidate Legato, and become increasingly angry when he keeps ignoring them. When Legato doesn't so much as acknowledge their presence, they shoot the fork out of his hand, and when Legato still doesn't acknowledge them (instead asking the waiter for a new fork), they fire additional shots around him. From there, Legato stopsignoring them...
There's also the episode 'Quickdraw' in which an official with few morals hold a small boy and his mother hostage to force Wolfwood to kill Vash for him, since he recognizes the hazard of going after Vash outright. Problem is Wolfwood is actually the more dangerous on an average day, and if Vash hadn't been there a lot of the guy's deputies would probably have died.
Also the time Vash takes on a bank robber gang without his gun, and every single person in town turns out to be armed because of a Chekhov's Gun incident mentioned earlier in the episode. They just needed his example to make a stand. (Incidentally, the baddies are using his name here.)
And people really ought to expect this every time they attack the infamous Vash The Stampede. That lynching scene with the truck—are you stupid? You're lynching the guy because he blew up two cities and a chunk of the moon! What do you think is protecting you?
That time Vash was taken hostage by the vengeance people, nonlethal example. Possibly also the resolution of the sandsteamer thing. Vash gets underestimated a lot.
Ax-CrazyPsycho for HireBlood Knight Kurudo Akabane of Get Backers fame gets so much of this. People have attempted to mug and antagonize him so many times...including, occasionally, the protagonists. Considered that Akabane is considered one of the, if not the, most powerful characters in the series' universe, it usually ends pretty badly for the muggers.
This is actually how Robert E.O. Speedwagon (stop laughing) and Johnathan Joestar meet and become friends. John is looking for the antidote to a poison in a rough part of town and is accosted by a gang of thugs led by Speedwagon. John gives them a speech telling them that no matter what, he's getting the antidote, so they best move on. As a display of resolve he takes a knife through his hand and Speedwagon declares him to be his new best friend on the spot.
Later on, a senator has the misfortune of having his car commandeered by Dio Brando and tries to push him around by mentioning how important he is. Dio is not impressed.
How many times has this happened to Kenshiro from Fist of the North Star? Every page. Every single page. Everywhere he goes, he is instantly attacked by crazy maniac Road Warrior people whose destiny is to literally explode after he strikes them. You would think word of this man would get around. Although that would require some bad guys being left alive to spread said word. Given what usually happens to them when they mess with him... yeah.
Rei is introduced this way, although he does it on purpose. By putting on a hood and cloak, bandits mistake him for a woman (although how they can mistake anyone with that kind of shoulder and chest musculature for a woman is anyone's guess) and harass him, whereupon he promptly kills them and takes their supplies.
In Shakugan no Shana, some street thugs try to mug Aizenji in an alley. He promptly slices them in two with his BFS, and eats them.
Lina Inverse's stock in trade. The first series and at least one of the movies (Slayers the Motion Picture) begins with bandits trying to rob Lina. Magical butt-kickings ensue. She didn't get the title "Lina the Bandit Killer" for nothing.
Hellmaster Phibrizzo's attack on Lina after he screws up her casting of Giga Slave certainly counts. Pressing the attack after Lina remained standing led him to the realization that he'd just attacked the Lord of Nightmares (a.k.a. God) by mistake. Cue justified panic.
Worse in the novel. He reveals he had a back-up plan to destroy Lina's heart. He does so. Lina no-sells it. He realizes who he just attacked.
Death the Kid (the "son" of a Physical God) met the Thompson Sisters when they tried to mug him. As it turns out he was actually sent to find the sisters - as their violent actions had put them on DWMA's list of targets - but instead Kid took them on as his Weapons instead.
Also happens when Soul and Maka go to Italy and are harassed by some of the locals. Said locals end up in a heap. It doesn't get much better for them, since later they try more or less the same thing with the Demon Swordsperson Chrona. They end up having their souls harvested. Baaaad idea.
Late in the Chunnin Exam arc of Naruto, a group of shady types confront one of the competitors on his way to the arena floor for his fight and demand he take a dive because someone is betting on his opponent. Said competitor is Gaara. It does not end well for them.
Early in Bagi, the Monster of Mighty Nature, a motorcycle gang chases down what they take to be a woman in a trench coat. She packs quite a scratch, leaving all but Ryo wounded with no wounds herself.
In the "Water 7" arc, first, a band of one-shot pirates try to take advantage of the Galley-La company, only to get thrashed by the Dock 1 shipwrights. Then, the Franky Family try to rob the Going Merry — while Zoro is watching it.
Then, when Franky Family actually do succeed in their mugging (in this case Usopp) they ended up triggering the Straw Hats' Berserk Button, leading to one of the most massive beatdowns of the series.
Shortly after Enies Lobby, Zoro (of course) gets lost while trying to make his way back to the crew to warn them about some Marines in the area. Some random dudes try to rob him. After an off-panel beatdown they're quite apologetic and more than happy to help him get back to the crew.
In a flashback, Ace is shown being harassed by bullies as a small child, who are talking smack about Ace's dead dad, the former pirate king. Cut to Ace sitting on a rock, being asked what happened in town.
Dadan: A bunch of thugs were beaten half to death!
Ace: You mean they're not dead?
During a flashback very early in the series, we see some random bandit harass Shanks... who actually more or less ignores them to avoid trouble. When they mess with Luffy, however... Turns out Shanks is one of the four pirate Emperors, and Shanks is apparently the Badass Normal of the group yet on par with a guy that can (supposedly) destroy the world with his earthquake causing devil fruit power and a guy that is so powerful he literally can't die even if he tried to.
This turns into a Crowning Moment of Awesome when Luffy and Zoro play this out when Bellamy and crew beat them up before they get word that Luffy's bounty is 100M and Zoro is 60M. Luffy returns to show them exactly how he earned a bounty that large.
Then, after the timeskip, Luffy gets mugged by an imposter pirate crew claiming to be the Straw Hats. He knocks them out effortlessly. Earlier the same people were harrassing Nami and Usopp when he came later. Both promptly show them why you don't mess with them.
In the fourth movie Dead End Adventure, a young boy was given the Sadistic Choice to kill a pirate in order to help his ill grandpa. He sneaked on-board Merry, thinking this was the weakest pirate ship. But when he attempts to attack Zoro and later on, Luffy ...
Also in the Ice Hunter arc filler, the Phoenix Pirates attempted to drug the Straw Hats so they could bring them to the bounty hunter family, the Accino Family. They didn't expect that nearly all the Straw Hats saw through their deception easily.
In another arc (Dressrosa), a bunch of swindlers attempt to extort a blind old man out of his money by flubbing roulette; while the old man keeps winning, his hosts constantly tell him the opposite result. Sitting nearby, Luffy takes notice of this and points the old man to his latest win, thoroughly angering the swindlers and causing them to go on the rampage. Big Mistake, as their mark just happened to be Issho, aka Admiral Fujitora, one of the newer admirals to succeed the recently promoted Akainu and the resigned Aokiji. One sword draw later, there's a new gaping hole in the floor and the restaurant is down thirteen patrons (and one roulette table).
In the same arc, when Luffy entered the Dressrosa tournament to win the Flame Flame fruit, a competitor thought that he was a puny runt (not knowing it was Straw Hat Luffy in a Paper-Thin Disguise) and attacked him. Big mistake obviously.
In the first episode, Firo has his fingers cut off by a random beggar after he sees just how much money Firo is carrying around. The fingers in question instantly reattach themselves, and he asks: "Did you do this knowing that I am Firo Prochainezo of the Martillo family?" Following this, the beggar promptly has his face rearranged by his would-be victim.
Not to mention the two different would-be villains who, one immediately after the other, try to murder that one redheaded conductor, not realizing that he's everyone's favorite Sociopathic Hero Claire Stanfield. Bad idea. Really bad idea.
Also in the Light Novels, Monica encounters a couple of sailors on shore-leave that have rather ill intentions towards her. Not only does she slice leader's arm open, she does it so fast that they don't even realize she's the culprit (allowing her to play innocent bystander and point them to the nearest medical facilities).
Some school bullies tell Tirawit to jump as it's part of the "traditional Japanese greeting," but obviously so the change in his pockets will jingle. As the head guy closes his eyes and explains, Tirawat jumps about twenty feet straight up and then crushes the coins between his fingers ("And this is a traditional Thai greeting.") and makes them his minions.
Subverted hilariously by Kenichi after the end of D of D arc. Kenichi and co have returned to school after fighting their way through life-threatening battles against opponents who had the skill, ability and mentality to kill them. Kenichi is promptly approached by a group of incoming wannabe delinquent freshmen and shows the fruits of his training and experience by... averting his eyes and cowering away. Nijima and the Shinpaku alliance have to bail him out and Nijima expresses his disbelief that Kenichi can still be afraid of common thugs. Kenichi responds that he's still traumatized from all his years as a professional bullying victim.
In Angel Densetsu, it's a small wonder Ryoko or Ikuno still finds people bothering them. You'd guess that after beating up half the city's delinquents, the other half would smart up a bit.
A pair of hoodlums attack old, slightly chubby Doctor Reichwein, who promptly disarms the first and knocks the other unconscious with a headbutt. As he tells the former, while choking him out, "I used to train with the Swiss Guard!"
Also Japanese surgeon Dr. Tenma has the balls to walk into a bar frequented by neo-nazis and ask about the gang's boss. He wouldn't take shit from anyone.
"Death Glasses Takamichi" is capable of using air pressure to simulate the force of a punch from about 15 meters away without magic. The people on campus thus have tremendous respect for his problem-solving abilities... but not visitors to the school festival. They are all flattened in seconds when they refuse to stop trying to pick a fight.
Takamichi: You're rushing at me? You must not go to this school.
Random guys in a magic world bar also try picking on Negi thinking he's a weak pretty boy. Not so much.
In an episode, some random crook shoots Tao Paipai. Without warning. From behind. Tao Paipai deflects the bullet straight at the attacker with his hand.
In fact, this is how Son Goku meets several of his future friends in the first series. Both Yamucha and Oolong first attempted to rob or take advantage of him because he was "just a little kid", only to be taught very quickly that Goku is no one to trifle with. Fortunately for them, Goku will forgive almost anyone.
Goku's first visit to the big city has him accosted by a pair of thugs. After Goku takes down one thug, the other is more than happy (And scared spitless) to help him out.
In the first episode of the series, Bulma shoots Goku several times after he threatened her, although she did hit him with her car. The bullets barely hurt him.
During the Crossover with Dr. Slump, General Blue tries to prevent Goku from attacking him by holding Arale at knifepoint. It does work at first, as Goku doesn't know about Arale's strength either, but then he tries to kill Goku, and Arale sends him flying to Egypt.
The Red Ribbon Army's interaction with Goku starts out as this. They believed that he is just some kid and don't really take him seriously. It is not until he brings down Muscle Tower that they begin to see him as a true threat. After that, it becomes a clear case of Bullying The Dragon.
When Raditz first arrives on Earth he is accosted by a farmer wielding a gun. The farmer shoots him only to have Raditz catch the bullet and half-heartedly toss it back hard enough to kill him.
During the Saiyan Saga, Vegeta and Nappa crashland on an alien planet inhabited by Insectoid Aliens during their journey to Earth. The planet is ruled over by an Evil Overlord who usurped the throne and oppresses his people, and the two Saiyan warriors are promptly thrown in jail. After they get bored they decide to overthrow the tyrant and kill everyone in their path.
The Ginyu Force truly believed that Goku was just a little punk with a power of only 5,000. By the time he was finished with them, only Jeice was left standing.
Catapy deserves special mention for thinking he could tickle Goku into submission. It ends with him flying a couple hundred feet in the air.
Majin Buu, now a nice guy, is shot during a hold-up in a jewelry. Being a blob, he absorbs the bullet, spits it out, then playfully throws it back with enough strength to put a crater in the wall behind the crooks. Said crooks promptly gave up and surrender to the police. Gohan and Videl show up and strike a pose reminiscent of the Ginyu Force only to be completely confused about why the bad guys are surrendering before they beat anybody up.
In Dragon Ball GT, some kidnappers decide to get a ransom out of Bulma by kidnapping her daughter, Bra. Rather than the predictable result of drawing the wrath of her Saiyan father, however, Hilarity Ensues and they end up kidnapping Goku, who was recently aged down to about 10 or so. Goku being Goku, he ignorantly hangs out with them as they try (and miserably fail) to ransom him off. Finally, while driving around looking for a phone, Goku overhears them and flies off, only to return with a telephone booth he has casually uprooted. They wisely decided to drop the plan.
One unruly client wants to leave a restaurant without paying and beats those who try to stop him. Including the waiter, a guy who was nicknamed "the Black Reaper" beforehe got super powers. And the place was owned by Yakuza to boot. The only reason he didn't get zapped senseless or stabbed within seconds of his first punch was that Hei was undercover.
Also none-too-bright: Goons are meeting November 11 to arrange a deal. He brings a bunch of money as a down payment. They break off negotiations halfway through, and he goes to pick up the money and leave... at which point a thug slams his hand down on the briefcase and blows smoke in November's face. Whoops. He gets his arm frozen off. The second guy gets stabbed through the eye with the contents of a cup of coffee. Their boss tries to get away, but April causes a rainstorm and November froze his feet to the ground. November 11 gets his information, and said boss ends into a much more fatal than usualHuman Popsicle. See, that's why you should cooperate with the nice sociopaths.
Happens a few times in Kaze no Stigma, most noticeably when a guy comes up to Kazuma and Ayano as they walk through some street. Defeated in seconds. Also, since members of the Kannagi family are pretty strong, Ren easily beats one of his classmates older brother who happens to be sort of possessed by a youma.
In Blassreiter, young harmless Malek and his only friend Johann are bullied by the upperclass German natives, who look down on them for being immigrants. When Malek becomes an Amalgam, this turns out to be a bad move.
In the two-part episode "Jupiter Jazz", the same group of thugs try to mug Faye and then Spike. It doesn't end well for them either time, particularly since their leader makes the mistake of calling Spike by the name of his rival Vicious. By the time Jet encounters them, the badly roughed-up leader is sulking in an alley declaring he's done trying to rob out-of-towners.
Happens in at least another episode when a thug tries to mug Spike using a knife. He is dispatched with no effort whatsoever. Spike in general seems to attract this, because people just assume thin equals weak, and he's definitely not weak.
This is practically a Running Gag, as 95% of the time you ever see bandits (or arrogant feudal lords leading dozens of armed men), you know in five minutes they're gonna be scraped off the floor after meeting the Monster of the Week. The rest of the time, they'll last just long enough to harass one or more of the heroes. Sango is a popular target, being a beautiful woman living in deeply misogynistic feudal Japan, but her complete lack of superpowers doesn't stop her from slaying demons for a living.
A group of demon-slaying priests happened to run into Sesshomaru. It falls short of Bullying a Dragon because while they did know he was a demon, they were wholly ignorant of just how powerful he was.
The movie The Castle Beyond the Looking Glass features a group of bandits that attempt to mug Hojo while Inu-Yasha, Kagome and Shippo are passing by. This is after Inu-Yasha has had a phenomenally bad day.
Shippo: I'm serious, guys, you better apologize. Inu-Yasha: Too late. (asskicking ensues)
Armitage III: This happens to Armitage, in what is possibly her most dehumanizing and monstrous scene in the first OVA. They see a small woman and assume she's easy pickings, but once she drops her cloak and they can see the battle damage she sustained earlier in the series, they realize they've made a huge mistake.
Everything that happens in Yu-Gi-Oh! before the children'scardgames kick in revolves around this trope. Yugi frequently gets the crap kicked out of him or gets taken advantage by someone with decidedly evil intentions, and his tormentors then inevitably suffer the consequences when Yugi's Superpowered Evil Side challenges them to karmically-appropriate Shadow Games, which usually leave the loser dead or insane.
Happens any time in Yu-Gi-Oh! GX when somebody - usually an Obelisk student - thinks Judai is going to be a pushover in a duel because of his red jacket, indicating that he's an Osiris student (a status often regarded of as synonymous with "loser"). In fact, during the Rise of the Sacred Beasts Arc, Asuka was worried that Judai would be the first target because the first of the Seven Stars would obviously go after the Key Holder who was most visibly in Obelisk, and she was exactly right. Of course, this Trope applied then too.
In the first episode of the first season of Koihime†Musou, Kannu is accosted by a group of bandits. She beats them easily.
In Durarara!!, a panicked Nasujima tries to rob the first person he sees after running from Anri. The first person he sees happens to be HeiwajimaShizuo. The same author created Baccano! (see above); it would seem he's fond of this.
Thug: Who do you think you are, Mr. Bartender... wait, bartender? Oh shit...
An odd example in the detective series Majin Tantei Nougami Neuro wherein a boy who is being horribly bullied decides to kill his bullies. In the typical style of the manga he uses a strange over-the-top method of murder by creating an animal-head shaped mask that sprays flesh-dissolving acid from the snout. However, when finding one of the boys, knocking him to the ground and attempting to melt his face he finds the boy just calmly smiling at him and talking through the melting bloody gloop that is his head. Turns out he just attacked Kaitou Sai, a shapeshifter whose already killed the boy and taken his shape so he could murder a pedophile teacher for the giggles. Strangely he isn't killed for this attack, instead the villain seems to agree with what he had done, reassure him that he had never bullied him since he had stolen the shape very recently and eventually basically hired the kid.
In Eyeshield 21, when Sena and Monta try to get a table at the local McDonald's ripoff so they can start talking about who should be in the Japan National Team, the guys they ask to move basically tell them to screw off and start taunting them. But wait a minute... OH SHIT they're Deimon's Superstars! AND THEY'VE GOT SHIN, GAOU, AND AGON WITH THEM! RUN!!!
Kenpachi Zaraki vs Nnoitra Jiruga. Nnoitra ripping off the eyepatch is probably the biggest mistake in all of anime.
Also, when normal people try to beat up Ichigo, he usually wins. Even when he's unrealistically outnumbered. This is somewhat Truth in Television as in real life, when regular joes try to gang up on a battle hardened soldier trained in The Spartan Way (like Ichigo and his repeated Training from Hell) they tend to get crubstomped. Almost uncanny spatial awareness and an almost animal battle instinct are almost mandatory side effects for people like that, because if they don't have it, they die. Of course, they don't win perfectly every time effortlessly like he does.
As a beautiful woman in a crapsack and crime-ridden post-feudal Japan, Oyuki, a.k.a. Lady Snowblood, is frequently targeted by would-be rapists. They do not survive their attempts.
In Digimon Frontier, Sagittarimon tries this on the digidestined, but they are saved by Angemon. Still, he comes back with some Centaurmon to back him up, only to be beaten up by the digidestined.
Hanaukyō Maid Tai episode 5. While Taro and Konoe are out of the mansion they're approached by three thugs who proposition Konoe and grab Taro. Konoe responds with martial arts attacks that quickly drive the thugs off.
Anyone who attempts to rob the home of Irene "Rally" Vincent will quickly learn why breaking into the residence of a gun shop owner/bounty hunter and the lover/apprentice of the mob's #1 bomb specialist is a very bad idea.
Then there was that guy who tried to steal Bean Bandit's cargo from him. It's amazing how many people keep trying to double-cross or con him, even though it's common knowledge that entire gangs have disappeared overnight after trying to make a fool of him.
Kumiko Yamaguchi of Gokusen is very short and thin. What idiots who attack her don't know is she grew up in a house full of Yakuza who taught her how to fight.
Semi-comic example from Science Ninja Team Gatchaman episode "The Secret of the Birdstyles". Jun goes out by herself as bait for Galactor agents. Two men, one armed with a knife, force her into an alley. We hear sounds of a beat-down, then she comes out unharmed and gripes, "Just a couple of street thugs. I thought they were Galactor!"
Some street punks mistake Gajeel for his wimpy alternate-universe counterpart. He kicks their asses.
An even better example occurs post-timeskip, in which Makarov has a meeting with the Guild Master of Twilight Ogre, who was dumb enough to think Makarov was just another dwarf-sized old man, and from that tried to extort money from him. It especially didn't help that Makarov brought Erza and Mirajane with him to said meeting. In this case the Guild Master of Twilight Ogre had already pushed their Berserk Buttons, they went there to talk and calmly repay the debt of them destroying their propriety and hurting their Guild Mates for 7 years.
During an episode of Last Exile, the crew of the Silvana end up having shore leave at Walker Palace, conveniently at the same time as the crew of the Anatoray battleship Goliath. Thinking of the newcomers as average renegades, the Goliath crew make the mistake of picking multiple fights with the Silvana bunch, leading to a brawl between the two crews. This brawl is only stopped upon Alex's entrance, but upon his attempt to call it off, the Goliath captain makes the even bigger mistake of throwing his glove at Alex, instigating a duel. Needless to say, when the Goliath people realize that they just picked a fight with the legendarySilvana (literally known as "Kill Em All Silvana"), and the captain himself realizes that he just talked down to the one and only Alex Row, the expressions are just priceless. And then they made their last mistake by trying to shoot the Silvana in the back, before the order to fire was given... making them the ideal test subjects for the Silvana's new jet propelled shell cannons.
Most Gundam series start off like this: the antagonists invade the colony that the protagonist faction is testing the resident Gundam in, whether to search out for said Gundam or to attack the colony itself. After the antagonists make mincemeat out of the defending forces, the main hero will "accidentally" end up in the Gundam's cockpit and activate it. The trope kicks in when the antagonists notice the Gundam's activation and, thinking it's like any other mobile suit, attack it... only to realize that their weapons can't penetrate the Gundam's armor, and much more the Gundam is packing more heat than their suits.
A slightly more realistic example happens in Kodomo no Jikan. It's revealed that the previous teacher was a serious Jerkass who insulted, cussed out, and generally made all of Rin's class miserable. Then his torment of them made her friend Mimi stop coming to school. She proceeded to harass him so much that he quit and was seriously ill because of it. The Aesop? Don't fuck with Rin, she's willing to ruin (or end) your life.
In one chapter, some sex slavers try to kidnap Veronica. She slaughters them all and leaves their informant alive to explain the mess.
In another chapter, some thugs attempt a school kidnapping, while Veronica and Gavrill were there (The latter as a replacement teacher). Terrible idea for them, as it was delightful news for Gavrill, who's been holding back her lust for bloodshed the entire chapter.
Black Lagoon. At first, people in Roanapur tend to seriously underestimate the Lovelace family Meidos, Roberta and Fabiola. Since either of them could give the Terminator a very busy, bad time, things get interesting really quickly whenever this happens.
Likewise when the Florida mafia tries to intimidate Eda by shooting the church door next to her. Even if Revy wasn't there, it's still a church full of gunslingers that run local arms dealing. Made worse by Lobos (who does know better) constantly telling him not to shoot at anyone.
Chaka also did this with Revy. Eager to engage her in a gunfight, he decided to provoke her by beating the shit out of Rock and later brags about having a body count that she passed years ago. Needless to say, it does not end well for him.
This has happened to Toriko twice. The first time, small-time gourmet hunter Zonge tried to bully him into giving up some drinks on a train...only to be scared off by Toriko's Awesomeness. The second time was when the heroes enter the kingdom of Jiddal and are accousted by some toughs. This time, Toriko is actually excited that normal people are picking a fight with him (As it doesn't happen normally) and scares them off by catching a bullet between his fingers.
In the prologue of Bokura no Kiseki, a group of upperclassman bullies choose protagonist Harusumi as their next target. He puts up with it at first, but when they go too far, he nearly ends up attacking them with magic that would certainly have killed them. In the end, he ends up knocking them out with a weaker spell, in the process freaking them out too much to ever mess with him again.
In Cat's Eye, the Kisugi sisters are attacked by crooks or other delinquents in multiple occasions. As the Kisugi sisters are also Cat's Eye, the titular group of Phantom Thieves that can steal anything and are combat trained, physically stronger than the average man and extremely agile, the delinquents are lucky if the sister they bothered simply steals their belts and tells Toshio (a police officer and boyfriend of the middle sister) they harassed her.
It's almost a Running Gag in City Hunter: one or more crooks will harass one of the protagonists or a recurring character only to discover the hard way that the two less dangerous ones are a tomboyish woman who carries an Hyperspace Mallet and multiple grenades and can beat up grown men bare-handed and a gorgeous woman who is a former cop and a Magnificent Bastard and carries a .357 Magnum handgun.
The most epic example is in a filler chapter, when a shotgun-wielding bank robber tries to take refuge in the Cat's Eye Cafe (a coffee house whose owners are two Hitmen With A Heart) while one of the owners was away but the one who was there was the gigantic Umibozu and our protagonist Ryo was helping him. As soon as they decide that Umibozu should deal with him, the shotgun has the barrel bent.
In the third season of Tenchi Muyo!! Ryo-Ohki, Misao Kuramitsu thinks attacking earth is a walk in the park - after all, it's just some backwater garden planet (as far as he knows) and his private ship could defeat the entire first fleet of the galaxy police. Turns out, when the two crown princesses of the biggest empire in the galaxy (and the intelligent flagship of said empire, the most powerful ship in the galaxy), the space pirate who managed to cause havoc in said empire single-handedly (with her ship, which is still pretty powerfull), the greatest genius in the galaxy, as well as some other people who you really shouldn't make angry all live on the same planet, then said planet is relatively save.
Justified in Assassination Classroom. Every single one of Class E's students is being taught by a Chivalrous PervertEldritch AbominationSmiley Face known as "Korosensei" (the name reads as 'unkillable teacher') in the fine arts of assassination...specifically, he's teaching them to attempt to assassinate him, a monster who has a slew of defensive tactics, inhuman special powers, and a speed of Mach 20. However, the assassination training is supposed to be kept a secret to the world, so the 95% of the school that isn't Class E still pick on the hard-luck cases and trouble children from that group.
Takaoka thinks that Nagisa, a small, shy, and sincere Class E student, will be an easy target to beat up and humiliate in front of the entire class. He quickly becomes the victim of a nasty surprise when Nagisa nearly slits his throat simply by walking up to him and taking him down with a clothes pull.
When a group of the school's 'educational elite' attempt to intimidate other members of Class E during test finals, the upper-class students make the mistake of saying they should risk their lives on the wager of the outcomes of the tests. Instantly all five 'elite' students find (thankfully blunt) objects jabbed into their jugular veins the moment they finish speaking, courtesy of the Class E students.
In Kill la Kill, when Ryuko Matoi first comes to town, she gets her pocket picked by a kid. She finds him, and he calls in his friends, thinking she is a helpless girl. She isn't, and they soon bow and beg for mercy.
Happens surprisingly often in Kyou Kara Ore wa!!, with people picking a fight with the wrong guy without knowing it's someone who can and will kick their ass. Justified with people who aren't students or from Chiba (and thus don't know Mitsuhashi and Itou) or pick a fight with Riko (her short stature hides her mastery of Aikido very well), but local school-aged punks should recognize on sight the distinctive hairdo of the guys who sent a Yakuza to the hospital and stormed Akehisa High (a school where the local Gang of Bulliesincludes the whole school and is justifiedly feared by any student in town).
A thief once broke inside Mitsuhashi's house and tried to steal his wallet, having no idea of who he was. Hilarity and a Chase Across the Town Ensued before the poor thief got a bucket to the head and was given to the police.
In Date A Live, Kurumi Tokisaki is walking home from school when she runs into three thugs who drag her into an alley intending to rape her. Little do they know that she is a powerful and psychotic spirit. She stains the alley with their blood and walks away thanking them for the meal.
Detective Conan: Most main-adjacent characters who look like harmless high school students are terrifyingly competent in some form of martial art, though love interest/karate champion Ran probably holds the record for Most Failed Hostage-Taking Attempts. And of course, the protagonist looks like an undersized elementary school student, and is actually a genius outfitted with weapons that could have been stolen from Inspector Gadget. That goes well for so many criminals.
In Blue Sonnet, the titular character finds herself threatened with box cutter-wielding juvenile delinquents who want to steal her lunch money under the impression that she's a sheltered foreign rich girl when actually she's a tank-busting supervillain who grew up in the worst part of New York City. The trope is averted because she doesn't want to blow her cover and so hesitates long enough for a not-strictly-necessary rescue to show up. The motorcycle gang earlier in the movie were less lucky.
Happens in Fullmetal Alchemist: Serial killer Barry the Chopper attempts to acost and attack a young woman walking home late at night. What Barry doesn't realize is that the young woman is one 1st Lt. Riza Hawkeye, who is a war vet and experienced sniper.
In Heavy Object a band of kidnappers call Froleytia's private line to try and ransom her daughter. It turns out they had the wrong number and managed to push every one of Froleytia's buttons while giving her a legitimate excuse to send her soldiers after them. When the caller realizes he has the wrong number, he hangs up while wailing in terror.
High School D×D: Issei runs into this a couple times. Most notably, a Mook tries to challenge him one on one. Since the baddy is a shadow-based Elemental Shapeshifter, he seems to do okay. And then he attacks the child with Issei. Issei pulls the child to his chest, slams his Made of Diamond wings shut around her, and lights the whole building on fire. Phasing doesn't protect you from heat...