It happens almost at every issue of the Thunderbolts. Which is to be expected: having heroes who have been villains all their life up to 5 minutes ago, and heroes who are former villains playing the hero thing for completely wrong reasons (because of the action, because the government forces them to, because everybody else in the gang is doing it), they will almost never manage things as the steady heroes would do. The first team had Jolt to point them those things, as time passes this role is done by the first Thunderbolts to the new recluits, or by the actual heroes who join the team (such as Vantage, Nighthawk or Captain Marvel), or by other characters that happen to be next to them.
Ultimate Comics All-New Spider-Man #14 opens up its first page with Gwen Stacy's "CAPTAIN AMERICA, YOU ARE A JERK!!". She's in a warehouse, so the windows behind her are broken and disused, so it looks like she shouted so hard it shattered the windows.
This is actually a nod towards an issue of Uncanny X-Men, where Kitty Pryde calls Professor X a jerk. The positioning of Gwen in the panel's the same as it was with Kitty in that issue.
In the autobiographical graphic novel Persepolis, to avoid being confronted by guards over lipstick she is wearing, she accuses a nearby man of "humiliating" her (the man had earlier leered at her, which actually is an offence in Iran), causing the guards to arrest him instead of her, never to be seen again. Marjane's grandmother then scolds her for her callous actions. Marjane's actions were truly disturbing, taking into consideration that the accused man, being arrested in Iran, may have been tortured or executed despite having committed a trifling "crime".
Earlier in the book, when Marjane is a child, she and her friends hear that a classmate's father has been unjustly arresting others. They decide to get revenge - by driving nails into the classmate. When her mother catches them at it (thankfully before they find the classmate), she bluntly asks Marjane "How would it feel if I drove nails into your ears?" She then reminds Marjane that no matter what the father did, it's wrong to punish someone for something a relative of theirs did.
Also, one nun in the school in Austria criticizes the author for a minor thing. She retaliates by openly calling all the nuns former prostitutes.
Watchmen: The Comedian and Rorschach both live across the line, and the other heroes feel appropriately uneasy about them. And no one's exactly thrilled with what Ozymandias does either.
Interestingly (and to some degree, ironically) enough, the Comedian actually gives one to Dr. Manhattan after he protests his murdering a Vietnamese woman; he notes that Manhattan could have stopped him, but chose not to.
"Yeah. Yeah, that's right. Pregnant woman. Gunned her down. Bang. And y'know what? You watched me. You coulda changed the gun into steam or the bullets into mercury or the bottle into snowflakes! You coulda teleported either of us to Goddamn Australia... but you didn't lift a finger! You're drifting out of touch, Doc. God help us all."
Recently in his self-titled comic book, Sonic the Hedgehog has defeated Dr. Robotnik. Suddenly, Robotnik flipped out, tearing off most of his mustache-Sonic winced in pain seeing that-and collapsed, babbling incoherently. When Sally showed up and asked what happened, Sonic didn't know, saying he beat him like normal. Snively then walks up to them and says that Sonic didn't just beat Robotnik, he broke him. Snivley gives a Breaking Speech where he acknowledges, "eccentrics aside", Robotnik is a genius and master planner, having conquered the planet in a few years. He says that Robotnik was losing his mind as a result of Sonic being the one thing he couldn't figure during his decade long reign, and Sonic winning again just now finally pushed Robotnik over the edge. Snively then asked to be left alone to take care of his uncle. As a result, Snively denied Sonic the thrill of victory, and instead made him feel bad about what he did.
More recently, Mina Mongoose called out the Freedom Fighters for keeping NICOLE around, even after she was brainwashed by the Iron Dominion, during which time it was shown just how big a threat she could potentially be.
This ended up turning into a My God, What Have I Done? for Mina when she realizes her doing that allowed the wizard Ixis Naugus to take over Mobotropolis.
A later issue has Silver appear and accuse Antoine of being the Freedom Fighter traitor in front of Sonic. Sonic, tired of Silver's crap and already at wit's end due to Sally being roboticized and the aforementioned Antoine hanging on by a thread due to him saving the dethroned Elias from a bomb-loaded Metal Sonic delivers a painful What the Hell, Hero? by spin dashing him through a wall, dragging him to where Antoine is, then telling him to get lost.
Spider-Man ends up being so disturbed by Iron Man's morally dubious actions (such as imprisoning non-registered superhumans indefinitely without trial) during Marvel's Civil War crossover that he defects from the pro-Registration side to the anti-Registration side.
Hulk also gave one to Tony and the other members of the Illuminati during World War Hulk. Hulk wanted revenge on the Illuminati for trying to exile him to a supposedly peaceful world, though in reality he ended up on a very hostile world which he eventually brought peace to and found happiness on, only to have the very ship that brought him there explode, ruining the planet and killing his new wife. This was subject to a very blatant Author's Saving Throw when it was revealed that the ship couldn't have possibly ravaged a planet itself by exploding, rather one of Hulk's allies had tampered with the ship's core, resulting in the aforementioned catastrophe. While this is seemingly meant to absolve the Illuminati of their crimes, the fact remains that their original plan failed horribly, resulting in them more-or-less making the Hulk someone else's problem while at the same time handing the means to creating an Earth-Shattering Kaboom to those same persons in the same package. If we think about it, most of Illuminati has their moments of that. Not so long ago Black Bolt gets one about his plan to end a cosmic war from all his family, advisors, and Vulcan himself.
Lately a lot of X-Men issues have been dedicated to calling out Professor Xavier for his regular abuse of his powers on the people he cares about. Guess he forgot his Mind Over Manners.
Cyclops, despite being very harsh on Professor X, has done a lot of morally dubious things himself for the sake of maintaining the ever-dwindling mutant population. He's been called out on it by Wolverine of all people; Beast quit the team in protest over his actions and Nightcrawler was prepared to chew him out thoroughly before he died.
Though in at least one case, Wolverine's issue wasn't what Cyclops did, so much as the fact that he did it and still acted like he was morally superior. Logan just didn't like the hypocrisy, although recruiting the emotionally damaged 16 year old for the wetwork squad probably did not help.
At the tail end of the Teenage Mutant Ninja Turtles Adventures story "Dreamland", Future Raphael (the story is set in the year 2094, a hundred years after the series' present) and antagonist Verminator X are in the middle of a Mexican Standoff. Verminator taunts Raph, saying that the turtles are too heroic to pull the trigger (this is one of the continuities where the turtles don't kill). Raph shoots him. Mikey and Leo try to call him on it, but he refuses to feel guilty about it, saying that Splinter's teachings about not killing don't apply in the now harsher world, and that Verminator would have probably killed them all in the future if he hadn't shot him.
Oracle also got a rather epic calling out after Huntress realized her "missions" were really a covert therapy session. Offended that Barbara was trying to "fix" her, she left the team, but not without giving one last parting shot:
Huntress: You left Gotham because you wanted to get away from Batman's influence. But you turned out just like him.
During the Red Robin/Batgirl Collision crossover, Stephanie Brown delivers a rant to Tim Drake, after hearing he led the League of Assassins, about his hypocrisy and moral ambiguity. Then he admits that she is entirely correct, and he'll try to be better in the future. This is this trope when it actually works - Superboy did several subtle hints around this theme an issue (of Red Robin, not the preceding Batgirl) earlier.
Speaking of the JSA, the team (except Alan Scott, and he's not exactly happy about what's going on either) gives Atom Smasher this when he helps Black Adam wipe out the army of a dictatorial regime. Then they give Hawkman one because his methods of dealing with Black Adam's allies was too brutal. If you kill anyone ever, whether they were good, bad, or neutral, you can expect to get this from the JSA, especially Jay Garrick.
A nonverbal one occurs in the recent mini Beta Ray Bill: Godhunter. Bill has decided to take fatal revenge on Galactus for destroying the remnants of his people by destroying planets marked for his consumption with weapons confiscated from an intergalactic arms dealer. One race insists that they will fight Galactus rather than evacuate, but Bill (rather than let them go through a suicidal last stand) is convinced by said arms dealer to infect them with a bio-war agent and use the cure to blackmail them into leaving. They do so, but when next he tries to pick up his enchanted hammer Stormbreaker...he cannot.
Carol Danvers a.k.a. Ms. Marvel eventually gives the Avengers an epic verbal beating regarding the events of the infamous Avengers # 200.*
The story in question involved Carol being unknowingly impregnated in order for Immortus's son to escape from Limbo. As a result of this, reality starts coming undone and Carol ends up returning to Limbo with the guy who Mind Raped and raped her. The other Avengers see absolutely nothing wrong with this.
A later issue plays with it; when Wonder Woman raises the point to Superman again in condemning Batman, Superman points out that while he and she can afford to be a bit gentler in their methods seeing as their words and actions are backed up with superpowers, Batman is essentially an ordinary guy playing on the same playing field as them with what basically amounts to a handful of gadgets to compensate, and so needs to take a more sharp-edged approach or else he might be killed. Wonder Woman concedes that Superman has a point.
Kingdom Come Superman gets stuff sprayed in his eyes by criminals, blinding him. He takes a wild swing, hitting our Superman. He apologizes, saying he was aiming for the crooks, but Supes points out that if that punch had hit anyone else, they would be dead.
In Superman/Shazam: First Thunder, Supes gives one to the Wizard for choosing a ten-year-old boy as his Champion. To his credit, the Wizard seems to acknowledge the point, and asks Superman to mentor Billy for him.
Happens several times in the Squadron Supreme limited series, as the Squadron continue their efforts to take over the world. Most of the callouts are given by Blackhawk, but Amphibian gets in a few licks too.
God, you know why people hate you? It's not because you're mutants! It's because you're a bunch of %#@&@&%@& *($!$^&&!^$ #&$@$&$#@*!!!
He also chews out Colossus, much to Colossus' confusion.
Why am I also a *(&*? I was just standing here!
In Courtney Crumrin and the Monster Holiday, Uncle Aloysius receives one from an innkeeper for his failing to notice the emotional weaknesses of Courtney, which resulted in her trusting and being fed on by a vampire. The innkeeper points out that Courtney is just a child and has been forced to grow up quickly to take care of herself, while her uncle treated her "like a piece of inconvenient baggage" on the trip.
Courtney gives a few herself. Namely:
While the Fair Folk have pretty ambiguous morals, Courtney still chews out one for not caring that her "son" (a human changeling she raised as her own) is trapped in the human world and possibly going to be killed.
When Courtney discovers that Hermia had it within her power to find a loophole in the spell and clear said changeling's name (which would have saved the changeling from its death sentence), yet chose to remain silent because "I just wanted to be left alone", she calls her out on it.
When Courtney rescues one of her classmates from the fairy realm, he instantly starts complaining about how dangerous it is and how the warlocks in the human world should go in and destroy it. Courtney points out to him that they are the intruders and that if he had listened to her instead of barging in and assuming that it was "Disney land meets Lord of the Rings", they wouldn't be in the mess they're in.
The Punisher gets called out by almost every hero (and a few villains) he comes across.
Hercules did this to Wonder Woman during One Year Later after he found out that she had run away from being a superhero.
Wonder Woman gets a huge one when she kills Max Lord.
And pretty much the entire Justice League (minus Wonder Woman who didn't know, and Superman because MAYBE he didn't know) gets one from Batman after finding out about Identity Crisis.
Superman was given by one of these in the wake of the New Krypton event, in which a woman chewed out Superman for being offworld when her husband died of a brain tumour, claiming that he could have saved him. This apparently led Superman to attempt to reconnect with humanity by Walking the Earth. There has been some issue taken with the woman's rant. Firstly, readers are skeptical that Superman's heat vision is superior to all medical technology for the purposes of removing inoperable brain tumours. Superman helps humanity purely for selfless reasons, making chewing him out for not saving a specific person seem just slightly ungrateful. And Superman was occupied at the time trying to prevent a war between New Krypton and Earth, meaning that he was in fact still dealing with humanity's problems. And finally, the New Krypton event ended with humans blowing up the planet, killing most of the Kryptonians. Meaning that the woman is yelling at him for being distracted by humanity committing genocide against Superman's species. In short, it's odd that Superman's reaction was to decide he needed to reconnect with humanity, instead of having to restrain himself from demonstrating the effect of Kryptonian heat vision on the human brain.
Some of this is lampshaded in the example, in that the other people around when the woman lays into Superman point out in Superman's defense that it wasn't exactly as if he was just dicking around twiddling his thumbs as her husband died.
It's also not explained why the woman's chewing Superman out when there are other heroes with abilities perfectly capable of removing the tumor. Atom can shrink small enough to travel phone lines and can make various gadgetry, Dr. Fate and at least two others have strong magical powers, and depending on the writer, other heroes' powers could apply.
Spike: People are dead, Prime! People that wouldn't even be dead if you Transformers never brought your war here! That's the bottom line!
In one of the the IDW All Hail Megatron universe, the Autobot Sideswipe calls out the other Autobots after Sunstreaker "sacrifices" himself to stop the insecticon swarm, for abandoning Earth to the Decepticons. However, it mainly falls flat when Optimus Prime has been rescued from death yet again, and retakes command.
This has happened with Wonder Woman a lot after she killed Max Lord. It seems like every character is attacking her for this even though it was the reasonable option at the time. This reached amazing levels of Informed Wrongness - with almost no one willing to give Diana (who was universally beloved hours before her actions) the benefit of the doubt... especially Superman and Batman, who saw the whole thing and knew what little choice Diana had.
In Fantastic Four, Reed gets called out by Sue for deliberately placing his son into a vegetative state. Granted, it was to keep his powers from going out of control and possibly preventing the destruction of every living being in the solar system, but this act disgusted his teammates enough for them to leave the team. Ben Grimm even says that it was "the end of the Fantastic Four."
In X-Force, Deadpool openly states that Fantomex killing Kid!Apocalypse was wrong. While Fantomex was the one who pulled the trigger Deadpool is upset that the team he joined supposedly to help make the world a better place crossed one of the few lines he never crossed as an amoral mercenary.
In one of the Black Widow graphic novels, Natalia encounters two thugs, and she warns them that if they don't stand down neither will ever walk again. She kills one and renders the second unconscious. The What the Hell, Hero moment occurs after she proceeds to fulfil her promise by breaking the back of the unconscious survivor, causing a male companion to have a Squick moment which she shrugs off.
In the last year of Outsiders, Geo-Force (who is both a king and a superhero) has been treating the team as his subjects, and specifically using them as a Markovian special forces team. Black Lightning finally gets fed up of repeating What the Hell, Hero?, and takes half the team back to America.
Cyclops has given one to Magik in New Mutants, on the account of the fact that in her personal vendetta against Elder Gods she manipulated her friends and teammates, almost got them killed and risked the destruction of reality itself without second thought and probably would do that again if she had to, which is the reason why they cannot trust her anymore and she must be restrained, until she'll prove herself not to be danger to the team and all mutants on island. Later, through it happens off-panel, Colossus clearly has told Scott what he thinks about not only the whole idea of restraining his sister but also the fact that he has took most dangerous members of the team to take her down in case she wouldn't accept his terms and send everybody who are emotionally attached to her, one way or another, on a mission, so they wouldn't interfere.
Dani, about Peter's discussion with Cyclops: There was a lot of shouting.
In X-Men's main series this is followed by Kitty tearing Peter a new one for trying to justify Illyana's behavior and not accepting that she is not as innocent as she used to be. Then Peter gives Scott another one again, for planning to make Illyana new avatar of Cyttorak, a.k.a. The Juggernaut but Scott lists several arguments at his defense. And then Kitty gives one to Peter again, for becoming new Juggernaut. Also, Cyclops gives one to majoyr Sadie for planning to destroy Utopia in the case X-Men won't stop Juggernaut.
Superman is horrified at Wonder Woman's behavior in DC The New Frontier when he learns that Wonder Woman didn't stop a group of Indochinese women from killing the the men that murdered their families, held them captive, and repeatedly raped them... Only to have Wonder Woman throw it right back at him.
Wonder Woman: These women have reclaimed their home and their dignity. I've decided to train them to survive the oncoming war. Surely you see the virtue in that.
Superman: You're supposed to set an example! But to allow cold-blooded murder, and then to celebrate...
Wonder Woman: What, hand them a smile and a box of flags? Their families, their mates... their children were murdered before their eyes. This is civil war. I've given them freedom and a chance for justice. The American Way. Take a good look around. There are no rules here. Just suffering and madness. I want you to go tell your undersecretary that. There's the door, spaceman.
Wonder Woman gets one in return when she returns to the States, learning that she nearly caused an international incident because of her actions, forcing her to realize that barging in to everything all willy-nilly won't work anymore.
Parodied in X-Men, when mutants has to team up with Future Foundation and this exchange occures:
In the BOOM Comics revival of Darkwing Duck Gosalyn and Launchpad learns the reason why Darkwing gave up being a hero was because Negaduck had learned his identity and was upstaged by a bunch of robots and decided to keep Gosalyn in a fancy school. Gosalyn reads him the riot act:
Gosalyn: I'm sorry, dad, but I've waited a year and a half to say this, but... [[spins Darkwing's chair]]Are You Crazy?! You're always saying "Let's Get Dangerous"! Not "Let's Get Dangerous Unless They Find Out Where We Live"! And certainly not "Let's Get Dangerous Until We Can't Afford It!"
In issue #9, Dream catches up with Death as the latter is feeding bread to pigeons. After a little small talk, she throws her baguette at him and yells at him because during his 70 year imprisonment he could have summoned Death at any time to help release him, but he let his realm go to crap for decades because he was too proud to ask for help.
Captain America gives one to Cyclops at the end of Avengers Vs X Men after the latter tries to Spin the restoration of the mutant populace into a victory, despite the damage caused by the entire fight.
In a crossover between Tomb Raider and Witchblade, Sara Pezzini, a police officer, gives Lara Croft this when she witnesses Lara cold-bloodedly shooting two guards. Lara's reaction is to handwave away Sara's discomfort and offer to leave alive the next guard they find so he can be arrested.