Subverted in Phoenix Wright: Ghosts of the Past. Phoenix was going to give one to Iris after she punched Trucy in the face(It was an accident, but he didn't know that yet), but when he saw that she was already in full My God, What Have I Done? mode he changed his mind and tried to help fix things instead.
In Feverish, America calls out England on forgetting who a very ill Canada is. England gets his chance later, when America storms the Canadian embassy and attacks several employees, without considering the consequences of his actions. And England, America, and France call themselves out constantly on overlooking symptoms of Canada's increasingly-dangerous sickness.
Willow gets one each from Xander, Cordelia, and Buffy in Echoes of the Fallen after she casts the spell to re-ensoul Angelus. Xander because he explained what a bad idea it was and made Willow promise she wouldn't try the spell again. Cordelia because Willow lied to her and Oz that Xander said it was okay for her to try again. And Buffy because Willow's actions forced Buffy to send the man she loved to hell.
In Variations on a Scene, Xander bitterly calls out Buffy over never thanking him for saving her life after she uses him to make Angel jealous.
In the Sonic the Hedgehog and Sailor Moon crossover Chaos Infinity, the Sailor Scouts force Sonic and his friends to fight them after they accuse them of the mess going on in Tokyo. (It's Eggman's doing, obviously.) After the showdown, Sonic holds nothing back as he berates them — just when he thought that they could look past animalistic looks. His words hit close to home:
Sonic: Ya know, when I first met these girls, the Sailor Scouts, I thought for sure that there were humans out there that weren't as vile and disgusting as Eggman… but I guess I was wrong for once.
Unintentionally given by Jor-El's recording to Asuka when she hears that he hoped that her powers turned her into a beacon of hope among the Earth's people. She feels horrible because up to that point she had used them to show off.
An hallucination masquerading like Superman gives her a much more brutal and direct one during her Mind Rape illusion, which completely breaks her.
Cole MacGrath: What were you thinking? Were you really going to kill her, Kitty? You really got to watch that sense of distrust you have. That gun you pulled at her, it's not something you aim at a teammate. When are you finally going to grow up, Kitty?
In the end chapter of To Kill A Thief, Light calls out Miyako about why she refuses to believe Maron is Jeanne because of the resemblance, contrasting on how he immediately fount out because of said resemblance.
In Stargate Equestria, O'Neill rips Rainbow Dash a new one for going off alone when he instructed her to take a partner.
Firefly berates Fluttershy for refusing to fight the griffins in chapter 3. Luckily, by the end, the issue is done with.
Firefly: Wake up, you moron! Didn’t you hear what they said?! They planned to kidnap little fillies! Those kinds of actions outright prove how evil they are! And yet, you still think they are not?!
In chapter 12, Firefly gets such a moment from Lightning Bolt, who calls out on her after she yells at Rainbow Dash while she's suffering from a Heroic B.S.O.D.. Brief, but powerful:
Lightning Bolt: Firefly, we need to talk! How could you be so harsh toward Rainbow Dash? She’s going through personal hell! We should be helping her... but you only keep yelling at her and everypony else instead!
Shepard gets called out aboard Farsight where a clone commander believes Shepard is responsible for killing her sisters when in reality it was Jakobs and their kill switches that did it. Of course, given that said kills switches are likely to be activated in Shepard's presence, she's not too happy that Shepard insists on sticking around to try to remove said kill switches.
Escalated with Caitlin Flanders, who calls out the Trans-Galactic Republic for using questionablemethods to obtain information that wasn't there to begin with.
To top it off, experiments with cloning have been unproductive at best, resulting in deranged lifeforms that can hardly be called useful or sane, but are shown to suffer anyway. Flanders refuses to participate, but that doesn't affect the program.
Part 4 has a double example: Rainbow Dash gives a scathing one to Fluttershy for testifying against her, telling her she never wants to see her again. When Fluttershy runs off in tears, Phoenix admonishes Rainbow, telling her she went way too far.
In White Devil of the Moon, Mars, Jupiter, Luna, and Tuxedo Mask get called out by their teammates for attacking Fate after mistaking her for a Dark Senshi. The group is trying to reach out to Nanoha and recruit her to win the war against the Dark Kingdom, but as the other Senshi point out, attacking Fate makes it more difficult for Nanoha to trust them. Hayate points out that she could charge them with assaulting an officer, but decides to offer them the same treatment given to other repentantformer villains in Nanoha.
In Suzumiya Haruhi No Index, Motoharu Tsuchimikado tells Aleister Crowley about Haruhi in exchange for Crowley legalizing marriage between Not Blood Siblings. Everybody who learns about this tears into him for it, including Crowley, who points out that Motoharu sold out God and potentially doomed the universe just because he wanted to marry his sister.
The Warmistress of Equestria: The Deer Seer Council is not too happy with Anlindē when her trip to Canterlot not only exposes the existence of deer to the Equestrians, but also coincides with an attempt on Celestia's life by Chaos-aligned assassins, and thus the deer are more involved in the brewing conflict between Equestria and the Griffon Kingdoms than the Council would like.
In The Boy With The Magic Notebook, while the Undersiders had to do everything they could to steal what they came to get from the PRT headquarters, nobody was on Imp's side when she hit Lily so hard upside the head she might've gotten brain damage.
Tony: What happened to your son is a tragedy. But you do him no respect by wishing his fate upon those he loves. If you truly care for him you would understand that he loves his brother and would not want to see him hurt. But don't listen to me. Wallow in your hatred. Let it warm you at night. Tell yourself you are the victim and wrap yourself in that indignation like a shroud. But don't make Jon your target ever again. Don't blame him for something that is not his fault. He will be my ward the next time you lay eyes on him and I do not take kindly to people insulting those I have pledged to protect. Speak that way to him again
Catelyn: You have no right to speak to me like this. You enter my home-
Tony: Which is only your home because you were willing to trade a dead Stark brother for a living one.
Catelyn: I am the Lady of Winterfell and my son... my precious son... is lying there and you DARE question how I treat that bastard? My son... my Bran-
Tony: Loves his brother. And he would be ashamed to see you like this. Of course, what he considers love and what you consider it might be two different things.
The Equestrian Wind Mage: During the Canterlot Wedding, Vaati actually takes time out of confronting Chrysalis to verbally rip the rest of the Mane Six a collective new one for how they treated Twilight, even going so far as say he doubts the Elements of Harmony would even work after they abandoned her.
Xander gives Willow a major one in Things Unseen, Things Unknown, and Things Yet To Be after he learns that she knows full well that the girl monitoring the security system is using it to get her own private peepshow and furthermore the magical cameras can't be turned off, not even the ones in people's bedrooms. Even worse is that Willow's idea of a solution is to tell the girl to "be more discreet". Xander later hits his Rage Breaking Point when Buffy and Giles aren't willing to fire the girl and instead put her on probation.
Wonderful: As in canon Worm, Sophia didn't try to help Emma when she was assaulted by several gang members until the red-haired girl tried to fight back. After rescuing her best friend, Taylor called Sophia out on her inaction.
“If you had moved in after she had gotten seriously hurt we would have having a VERY different conversation right now.”
Children of an Elder God: When Gendo finally reveals Asuka how her parents died and tells her everything about NERV’s genetic experiments, she's absolutely furious and asks how they were capable to do such a thing:
"How could you do something like that? That's horrible, going around altering the genetics of babies! How could you do that to my parents?"
During the third chapter, Ethan gets one from Cerberus agent Lynch when he appears at the scene to find what is essentially a failed mission, with Liara and Feron captured and Shepard’s body still with Tazzik. Earlier in the chapter, when Ethan attempts to bargain for information by taking a Centurion hostage, the other Blue Suns call him out on the unprovoked killing he has done before. Ethan rebukes this, calling them out on their Moral Myopia.
Liara's reaction was basically this when Ethan suggested handing Shepard's body over to Cerberus. He managed to convince her to see from his viewpoint, but it was clear that she was still upset about the whole ordeal.
Xander gives one to the other Scoobiesin Good Morning Sunshine when he learns that for the three days he was held and tortured by Angelus, Spike, and Drusilla, they simply thought he was home sick and never bothered to check up on him.
In The Return Of Dani Phantom, Sam gets called out by Danny for her insensitive comments about Danielle. Those hurtful words result in Danielle running away, getting captured, Danny heading in to rescue her, and nearly getting killed in the process. Needless to say, it comes back to bite her.
In The 10 Doctors, The First, Second, Second-and-a-halfth (Long story) and The Seventh Doctors give one to the Ninth as he almost sacrificed Rose in order to destroy The Supreme Dalek a.k.a. the daleknized Tenth Doctor
The dwarven noble gets some of these in Dragon Age: The Crown of Thorns. One of them leaves him with broken ribs and a snapped jaw. He expected it and let it happen, but it still hurt because healing magic didn't work on him until recently. And even now it's not a given.
Norm, of all people, calls out Timmy when he realizes that Timmy wished for Poof's existence, meaning the fairy infant would eventually be undone like all the kid's wishes whenever he lost his fairies someday. Amanda fixes that problem with a wish of her own.
In Forward, the crew calls Mal out when he spaces one of Niska's captured henchmen. A couple of story arcs later, Mal again gets called out for refusing to support Book's plan to save Simon's life by taking him onto an Alliance ship and using Book's ID card. And of course, Mal calls himself out on nearly every other decision he's made.
In The Fifth Act: Cloud is called multiple times throughout the story for wanting and attempting to kill Sephiroth for the actions done by original timeline!Sephiroth when Sephiroth is no near the monster the other one became thanks to Cloud's actions. Cloud later gets called out for attempting a murder-suicide with Sephiroth during the story's climax.
In Cissnei's Path: Cissnei chews Cloud out for working with AVALANCHE in bombing the reactors because not only did the collateral damage affect everyone from hospital patients to employees, but he was tarnishing Zack's memory.
In Frozen Hearts, these are exchanged when Prince Hans' brothers are discussing going to the king to ask for a pardon. The group in favor of doing so is accused of forgetting the seriousness of Prince Hans' crimes, as well as their impact on the kingdom. The group opposed to doing so is accused of forgetting that he is their brother, and of having some overly cruel ideas for punishment.
In Build Your Wings on the Way Down Hughes is angry at Roy for endangering an eleven-year old kid (Ed) in the train by having him fight terrorists, regardless if Ed is a talented alchemist because Ed was strangled and hurt and got have been hurt worse since Ed was by himself.
Hughes is angry at Roy for allowing Ed an attempt to save Nina if he believes with good reason that Ed will fail and kill Nina in the attempt.
Akio pulls Maho aside while they're visiting Miho in the hospital and expresses his belief that she is not there for Miho enough by saying "If I had a sister, I’d be there for her all the time. Not just when she’s in the hospital." Of course, he does so unaware that Maho's primary reason for being the Nishizumi heiress, which unfortunately forces her to be distant from Miho at times, is so that Miho can live her life her own way, and unfortunately, he persists in this opinion after Maho protests Miho being disowned and sends her money to cover her rent.
Akio, Maho and Miho'sfather all are quite upset with Shiho when she disowns Miho.
Snape:Why did you never save Tom Riddle from that muggle orphanage, Dumbledore? You must have known there was something wrong with him even then. Considering the time and place as well as many other factors... you left my Lord in a hell hole time and time again. You left a young wizard to rot in the middle of a muggle war. And why, in the ten years Harry remained with his relatives before Hogwarts did you never go and check up on your supposed Savior? Had you never seen the miniscule space he'd been forced to live in for ten years? The space under the stairs? Did you never see that there was nothing within the Dursley home to show there was in fact two boys growing up there?
In Unmade, after being locked in a Company cellwith Sylar for an indefinite amount of time, Peter comes to agree that when they get out of here, Sylar can slice up Adam (who "deserves it") for his regeneration power instead of Claire (his "innocent" niece). Sylar calls him on it: "It's bloodthristy... for someone like you."
Webwork: Jackie is less upset at the fact that Jade is now a pregnant spider demon than he is when Uncle informs him that Paco's attempt to cure her harmed the eggs she carrying, and her by extension, which he compares to hitting a pregnant woman in the stomach.
In Reconciliation, it is revealed that Lilly was angry with Hisao for disregarding her advice about Hanako, checking on her when she didn't want to see anyone, triggering the Bad Ending (in which Hanako angrily declares that she hates Hisao and Lilly) and leading to Hanako distancing herself from Hisao and Lilly for eight years out of guilt. Averted when Hanako expects to receive a response like this from Lilly, but does not.
In Mad World, Trick uses his powers to write that the Garuda will be defeated by a champion (who turns out to be Bo). The Garuda is aware of this, and knows that Lauren will be involved. So it and Thaneutterly destroy her life trying to prevent it. Thane murders 19 of her colleagues/friends, murders her, she is then brought back by the Fae, forced into slavery to them, and then Thane returns and subjects her to Mind Rape and horrific torture. She is distinctly unamused when Trick confesses his role in it, and calls him on it in the sequel.
Lauren: What right did you have to play God?
Lauren: I am so...sick of explanations of the greater good. I get it from the Ash, from the Morrigan, from you. Everything that happened is for the greater good. I am tired of my life being nothing more than a trivial after thought to you people. I had a life, a good life before it was taken from me. I died and was resurrected because that would help the Fae. I have lived the last five years at the mercy of the Light Fae while most of them treat animalsbetter than they treat me. So, to answer your question Trick, I'm not alright. I haven't been alright for five years and now I'm just sick of putting up with it.
Trick: Lauren, I'm sorry.
Lauren: Keep your apologies. If you want to help me, you'll write a new Fae future that I'm not a part of.
There's also a failed one. Lauren finally kills Thane (after said torture); Amara, while happy that Thane is dead, is deeply upset that Lauren killed him. She feels that a Fae who sacrificed himself to resurrect Lauren (who was also her brother) was of a pure and superior fae, and that Lauren has destroyed said purity by killing someone. It comes off as petty and arrogant given everything that has happened, which was likely intentional.
In Perfection Is Overrated, Mai explodes at Mikoto after she (while Brainwashed) kills Bachiko and Meiko while they're fighting Mai and acts like nothing has happened]]. Mai is less disturbed by the action than the way Mikoto acts with regards to it, especially considering that the enemies were SUEs with the power to alter their victims' personalities.
Mikoto: "Mai… What… happened here?"
Mai: "Don't play dumb, Mikoto! You killed Bachiko and Meiko, don't you remember?"
Mikoto: "I did? I don't remember. I saw you… in trouble… and the next thing I knew, the two of them disappeared."
Mai: (after a pause) "I'm sorry, Mikoto. I just… don't know what's happened to you. Obviously it's not the SUEs' influence, but you… didn't seem yourself in that moment. You're a kind girl who makes friends with everyone, not some ruthless killer, even if it's my enemy you're fighting."
In Mass Vexations, Author Avatar Art gets chewed out by Shepard for purposefully splitting a salarian STG unit on Virmire, thus forcing Shepard to make a choice between him and Ashley and nearly getting the salarian unit killed. And that's not including how he gets yelled at for insubordination.
And then, this trope pretty much kicks Art's ass all over the place in the sequel. Let's just say creating a Conveniently Unverifiable Cover Story and then hiding the truth from Commander Shepard was not one of his better ideas.
Garrus chewed Shepard out for rejecting him after he had abandoned everything for her while she had led him to believe that she did feel something for him (she did, but didn't want to admit it to him). They snapped, ended up fighting, and she decided to kick him out after they're done with Saren.
Thane called Garrus out for constantly shutting himself off to wallow in the past and ignoring Shepard after Garrus had promised to never leave her side again.
Dozens of MLP fanworks love to heap this sort of thing onto Princess Celestia for her actions throughout the series. Most notably not being the one to solve any of the conflicts in-show and never issuing an on-screen apology for her failures or shortcomings, especially after the Changeling Invasion.
In No, I am Not a Brony, GET ME OUTTA EQUESTRIA!!!, TD epically calls out the Mane Six sans Fluttershy for how they've treated him over the last couple of days: Pinkie punished him for breaking a Pinkie Promise - after he'd apologized - by setting him on (harmless) fire; Rarity cast a freezing spell on him to keep him from running out of the boutique when he thought she was going to make him something ridiculous - then used him as a mannequin - rather than simply explain that she would show him her designs and get his approval before making anything; and Twilight, Applejack, and Rainbow Dash attempted to beat the crap out of him less than an hour after he'd woken up in the hospital - admittedly, he had just punched Celestia in the face for accidentally bringing him here, but as he points out, their actions were completely disproportionate to any damage he could have done to an immortal sun goddess.
History repeats itself in Chapter 13, when Celestia informs him that she has no way of sending him home, despite her best efforts. While he tries to restrain his anger, a confrontation with the Princesses and Blueblood in the middle of the Gala gets out of control and ends with Celestia getting punched again and Luna snapping TD's spine in retaliation. After Celestia heals him, he silently returns to his house in Ponyville. When the Princesses show up the following morning, he rejects their offer of help and angrily calls out Luna on her actions:
TD: Thanks for the game of ‘head on a stick’ with me and the back of that chair. I always wanted to know how it feels to be a quadriplegic.
Luna: We... We are sorry for what We did to thee. Our reaction was disproportionate.
TD: You think? What's with you ponies and thinking Celestia needs protecting from me anyway? If whatever I do is unwarranted, then she can execute me herself.
The Pony Psychology series has an entire chapter devoted to Celestia lecturing Luna on the true consequences of the environmental and ecological effects of an endless night (with frighteningly accurate scientific references and detail), mostly in an attempt to quell any doubt that Nightmare Moon might have been doing them a favor.
In the My Little Pony: Friendship Is MagicAlternate Universe Fic, Rainbooms and Royalty, in which Rainbow is Celestia's personal student instead of Twilight, Rainbow directs this towards Princess Celestia after she and the rest of the Mane Cast defeat Nightmare Moon. She is enraged to discover how Celestia manipulated her and her friends behind the scenes since their foalhood in her plan to redeem her sister. Interestingly, she's not upset about being used, she's upset that Celestia did not trust her enough to be forthright about her intentions, because she would have gladly aided Celestia. She's also incensed that Celestia was willing to risk her and her friends to redeem Luna, rather than confronting Luna herself, and, if necessary, fighting her. She says that she still loves Celestia, but she cannot forgive her yet. Fortunately, after both the princess and Rainbow have a chance to talk with other ponies, they reconcile quickly.
In The Vinyl Scratch Tapes, Vinyl gets one from Princess Luna when Vinyl not only insults Prince Blueblood (who may be a jerk, but by that point Vinyl's campaign to get back at him was so successful he's turned to drinking to help deal with the fact that ponies send death threats to him on a regular basis) in front of her, but also reveals she's the one who humiliated Princess Celestia by guilt-tripping her for banishing Luna during her Nightmare Moon phase, causing Vinyl to enter a Heroic B.S.O.D.. Later, Luna is forced to apologize for the latter (but refuses for the former). However, Trixie then busts out of a trash can (It Makes Sense in Context) and accuses all the assembled ponies who gathered to make Vinyl feel better that they are all hypocrites for treating Blueblood like a pariah for being a jerk, but pretending Vinyl's own jackassery is charming (especially since this jackassery involves hiring a known criminal and a slaver and bringing him into the heart of Canterlot).
Rainbow Dash herself rips Rarity a new one in Episode 4 for blowing off her friends to spend time with Regal Rule. Rarity brushes her off, which makes her feel even worse when she has her My God, What Have I Done? moment later on and realizes Rainbow Dash was completely right.
In Jericho, the eponymous main character, Jericho, has this happen to him when he gets attacked by an angry townspony. In a blink-and-you'll-miss-it fight, Jericho knocks the guy out, only to have the guy's wife and little daughter both rush to his aid. They yell at him, and then he has a What the Hell, Hero? moment on himself.
Jericho: “Oh, you mean the side-neck chop? That’s just a martial arts move. I mean, yeah, if I’d done it wrong, it would have killed him via cardiac arrest, and so, in hindsight, that was highly irresponsible of me to do but... I’m not helping my case any, am I?”
In Team 8, Kurenai calls Hinata out on pushing herself as far as she did against Neji, which almost resulted in her death and upset Naruto to the point where he nearly forfeited his own match by being unwilling to leave her side, suggesting that she had no regard for her safety or her friends' feelings when she did so.
Naruto and Kushina trade these in Eroninja when they're sent to the past. Kushina (taking the place of the Kyuubi) suggests Naruto inform Minato about the future so they don't die and Naruto can grow up with his parents. When Naruto insists they can't as it's impossible to tell whether they can even change time and that if they succeed, the results would be unpredictable, Kushina angrily accuses him of sacrificing his parents to protect his harem lifestyle. Naruto retorts that she's asking him to sacrifice himself and his family for the sake of her and Minato. If Naruto was raised with his parents, he'd likely be a completely different person than he is now.
In A Father's Wrath, Orochimaru (Naruto's father in this fic) calls out Tsunade and Jiraiya when they meet again, asking them why they weren't around when Naruto was growing up and he needed someone to look after him and guide him.
Surprisingly, Inner Sakura calls out the real Sakura in A Growing Affection when she starts bullying Hinata.
Orochimaru calls out Tsunade in Of Ramen and Wooden Skates for constantly borrowing money from him and Jiraiya for gambling and never paying them back. Not only does she owe Orochimaru more than he makes in a year at his part-time job, but Jiraiya had to move in with him after he couldn't pay his rent.
Ino apparently gave Chouji one offscreen in Team 7's Ascension after his refusal to kill a downed enemy results in her being temporarily crippled and Akamaru killed.
From Misato to Asuka after the latter attempts to commit suicide.
Teri also chewed Asuka out via telepathy by nearly killing them both.
Asuka gave one to Shinji when he got so frightened, thinking he could not protect her, that he broke up with her.
A minor, humorous example when Shinji complains Asuka has gotten heavier, she replies it is Teri’s fault and he asks whether she is seriously blaming their unborn daughter who can’t speak in her behalf.
Evangelion 303: This doujin provides several examples. Asuka and Shinji were recipients of most of them:
In chapter 2 Asuka punched Shinji because during a training duel because he had pulled a suicidal move and he had got her nearly killed. Misato yelled Asuka that, even if Shinji's actions were wrong and punishment-worthy, striking a fellow pilot was completely unacceptable and it would not be brooked.
Meanwhile Ritsuko lectured Shinji that pulling suicidal moves during a friendly duel or training, only because you are determined to win, may be a stupid way to waste your life.
Saburo felt ignored by Kaworu and broke up with him due to a fit of jealousy. Kaworu moved on but Saburo did not, and he resented that Kaworu went out with other people. In chapter 7 he warned Kaworu against wasting his "forgiveness". Kaworu was not amused:
Kaworu: Forgiveness? You dumped me in a fit of jealousy fanned by the flames of your own imagination. There never was anything to forgive.
In chapter ten Gendo lectures Shinji about spending his entire free time watching over a comatose Asuka, and reprimands him for neglecting his duties and being more concerned with Asuka than with saving millions of innocent lives. Shinji replied that he knew nothing about "duty".
After Unit-04's crash and spending several months in a coma Asuka blamed herself for the failure of the mission and her friend's death, and she hated herself. To cope with her pain, she started to lash out at everyone, especially Shinji. In chapter 12 she is going through an inner turmoil and her rational side lectures her harshly about her actions:
Asuka: Nobody understands what I’m going through! Asuka: Do YOU understand? Asuka: ?! Asuka: Do you see what you are doing? What you’ve been doing ever since you woke up? You wrap yourself up in this warm blanket of hate because it makes you feel powerful! It’s the only way you can feel powerful again without the help of others! But it’s only a drug. A quick chemical that hides your troubles! Meanwhile they’re still there GETTING WORSE. So, once again, the great Asuka Langley Sohryu is retreating from her troubles armed with a medicine cabinet of powerful looking narcotics! My, how self-reliant you are!
In chapter 15 Asuka and Mari were supposed to take part in a training. However they started to to dog-fighting. Misato chewed them out, stating that she had no use for pilots that still have to prove that can do their jobs.
After Asuka turns his Love Confession down, accusing him from lying to her, Shinji says she shouldn't tell him how he's feeling, or treating her friends like that.
Shinji sat down, regarding Asuka with a mixture of hurt and anger. His fingers twitched, before closing into a fist. "You need to start listening to what I say," he said softly. "I may be an idiot, but I know how I feel. Better than you do, anyway." She nodded. "I don't mind being hurt sometimes," he went on. "That doesn't mean I like it, but I can deal with it. It means you're being honest with me and I appreciate that. But this morning, you went too far." "I know," she said. He leaned on the table. "When you got back from Kyoto, you said you wanted to be friends with me. Don't you remember that?" Asuka's eyes were watering. "Yes." "Is this how you treat your friends?" His voice was tinged with anger. "Are things really so terrible between us that you would say something like that?" She squeezed her eyes shut, tears rolling down her face, and shook her head. "I'm sorry," she said. "I—"
Asuka berates Misato for let her down and abandoning her right when she needed badly someone who cared for her.
Higher Learning: After Shinji left, encouraged by his teacher's words, Misato confronted Kaoru about it. When he accused her of treating Shinji as a war tool she said angrily she does not care about NERV and she cares about Shinji more that she will never care about Kaoru, but as long as the war lasts, neither of them has the luxury of leading a normal life.
In Poké Wars: The Subsistence, Tracy gets yelled at by the entire cast after he tries to assault Jessie, James, and Meowth after their Heel–Face Turn.
Pokémon: Take Two, a Send Your OCs fanfic, gives us one in chapter seven. Actually, that entire chapter is pretty much dedicated to telling our main character how much she sucks as a person, and how she really needs to get her act together.
In With Strings Attached, the four (specifically George) decide to abandon Jim Hunter to his mind-sucking BFS because they don't want to risk their lives trying to get it away from him. They feel guilty, but they do it anyway. Luckily for both him and them, the ruthless ploy results in Jim's being able to release the sword, so he thinks it was just a brilliant maneuver on George's part. No one is in any hurry to tell him differently.
Also, they refuse to rescue or even contact Lyndess after they deliver the Vasyn, pretty much saying that she can go fuck herself... despite her having saved their lives at the end of the First Movement.
The Massively Multiplayer Crossover (but mostly Ruroken) fic Blood And Revolution has Aoshi massacre the Cabinet and most of the Diet in 2015. Absolutely no one was happy about this and he was given various levels of confrontation for it - from Kenshin's "How could you...?" to Hiko's beheading him.
In Massages, the girls make Jaune give them massages, because he is really good at them. Ren calls them out on doing this whenever they feel like and running Jaune ragged, and on not noticing that Jaune's hands were slowly getting damaged with each session. They are deeply ashamed and apologize. Later, when Jaune gets kissed by Velvet, the girls get jealous and yell at him, only for him to point out that they don't have any right to decide who he dates.
Miya gets a couple in the early chapters Ashikabi of Thunder and Lightning. First, Uzume snaps after Miya scolds her for making a dirty joke. Uzume accuses Miya of bullying the other Sekirei into following her own "prudish lifestyle". While Miya is shown to have a point (sex before their power matures stops a Sekirei from growing stronger), Uzume is still upset that Miya bans all forms of sexual contact and refuses to share any information with the others even if it'd be useful.
Later, after Miya accuses Takami of using her own children as pawns, Takami angrily responds that as Miya has "removed herself from the board", Takami has been forced to do what she can to limit Minaka's mad schemes. Takami further demands to know just what will force Miya to actually become involved in things instead of sitting everything out.
The North Remembers: When Jaime Lannister is sent into a trap set up by the Brotherhood without Banners after being led there unwillingly by Brienne, he is given the standard Kangaroo Court before setting out to hang him. Like Sandor Clegane before him, he calls them out on this behavior, specifically to Lem Lemoncloak.
Jaime: “You smell marginally less bad, you potentially have better table manners, and you're more likely to be mistaken for the hind end of an aurochs rather than a goat, but for the life of me I can't see how you're different from the Bloody Mummers. At least they only had the decency to take my hand, but you won't be satisfied with anything less than my soul. Haven't you thundering imbeciles worked out by now that there's nothing there to give? Kill the Kingslayer, very well. Then you'll be a hero. Will that make you immortal, or set to rights the wrongs you're supposedly avenging, or do anything besides make you just as much a murderer as me? I don't care what god you pray to or what high-and-mighty purpose you claim. You still think you're the only ones to lose something in this war, and that makes you at least as blind as my sweet sister. Drop those breeches, Pisscloak, grace us all with the delightful aroma of your shit."
In The Legend of Spyro: A New Dawn, Sparx of all people calls Cyril out on him saying that rescuing the kidnapped eggs wasn't worth putting the rest at risk by dividing their forces... right in front of Cynder, who was in a Heroic B.S.O.D. over the fact her adopted egg was among them.
The Wrong Reflection: The fic is set a few weeks after a Noodle Incident (explained in another to-be-published fic) in which Eleya lost it at a conference and cussed out "three ambassadors, a rear admiral, and the Proconsul of the Romulan Republic." She avoided being cashiered outright by dint of being a Bunny-Ears Lawyer ("I kinda helped save Earth Spacedock after."), but she still ends up with a massive black mark on her service record that means she'll probably never make admiral. (Granted, she wasn't interested in being an admiral anyway.)
"Last Rights": Nobody ever misses an opportunity to call out the Kobali for using living Vaadwaur soldiers locked in stasis as reproductive stock (something they did in the canon Star Trek Online story).
In "Flaihhsam s'Spahkh", when the very anti-Federation Senator Vreenak says that the Federation cannot be trusted not to use the USS Defiant's cloaking device against the Romulan Star Empire, Morgan points out that the Federation has historically gone out of its way to keep the peace and that most of the violations of the Treaties of Alpha Trianguli and Algeron were the Romulans' doing.
Blood and Honor: Vette calls Sanguis out on her actions several times, questioning the Sith's unforgiving treatment of Jedi, disinterest in the welfare of Jaesa Willsaam, and participation in the entrapment and murder of a Dark Council member.
Beast Boy gets this a lot in the first two chapters of The End of Ends, though his actions justify the calling out (they range from stalking one school girl to raiding Raven's room to downright beating up two school girls), though since it's one of those fanfics, they're portrayed as the Titans being mean to Beast Boy.
He resurrects a friend for a job and fails to realize the friend is suicidal after the job is over. Ratchet and the friend’s young son call him out on it.
He doesn’t reveal that he’s become a Nay-Theist (he’s supposed to be a Priest King) until the revelation almost derails the crowning of the next Prime. Ratchet and the young son (now grown up) call him out on that, too.
He breaks into Optimus Prime’s office and then lies about having called ahead when he accidentally interrupts a private moment between Optimus and Elita-One. Elita, Optimus, and Megatron all call him out on that.
Transformers Victory: Leozack, of all characters, complains to Victory Leo when he's willing to leave Holi and Jean for dead.
All the main characters in Shatterheart gets one and at seperate occassions:
Real!Syaoran is called by Fai for keeping his relationship with Kurogane a secret from him and not telling Sakura the truth. In the Nihon Arc, Kurogane calls him out on his indecisiveness when he wanted Syaoran to make clear whether Syaoran would stay with him or Syaoran would continue to pursue Sakura.
Sakura is called out for treating Real!Syaoran like an non-entity and for shunning him for him not being his clone when Syaoran wanted to know her.
Fai is called out for hating and shunning Real!Syaoran and for emotionally blackmailing Syaoran to end his relationship with Kurogane, which at the time was his only positive relationship. Kurogane and Syaoran let him have it when they find at the end of the Infinity Arc he was going to backstab them the entire time.
Kurogane is called by Fai for agreeing with Syaoran's offer for a sexual relationship because the latter was emotionally vulnerable and still in love with Sakura. After he breaks up with Syaoran, Fai calls him out on the brutal way he ends their relationship. In the Nihon Arc, all his friends call him out that he lets his anger get the better of him and he doesn't let himself feel his own emotions when he brutalizes Syaoran and misses the obvious cues that Syaoran was trying to calm him down.
Yu-Gi-Oh! Forever: Yugo (the main character and the son of Yugi) gets called out on three separate occasions by different characters:
The first time, one of his Five-Man Band snaps at him for behaving like a Jerk Ass toward their mutual friend and for attacking her during their duel, in such a way as to potentially cause her injury (which Yugo did because she inadvertently pushed a sensitive button for him).