The "Kallen Combo"◊ would count as an example of calling (a guy who claims he is) the hero out on his actions. Suzaku tries to apologize to Kallen for trying to forcefully drug her to get a confession out of her. Her speech (in between punches) can be summed up with this trope.
Episode 19 of R2 has the entirety of Black Knights (except for Kallen) doing this to Lelouch when they hear it from Schneizel: Lelouch has constantly lied to them, hid the fact that he was a Britannian prince, killed their allies, was responsible the SAZ massacre, and supposedly used Geass on them (although to be fair, they were wrong about that last one, and the SAZ massacre was an accident and Lelouch actually felt tremendous guilt about it, also the reason Lelouch hid his identity was reasonable, as the Black Knights would have betrayed him, if not kill him, on the spot if they realized he was a Britainnian prince, had various yet critical facets of everything but the first obfuscated by Schneizel, and themselves deserved a good What the Hell, Hero? for their haste in the whole situation and Moral Dissonance in taking the word of another Britannian prince and the most prominent one at that, who just launched a nuke at their own country for good measure, almost immediately). The result is that he loses his entire army.
In the Grand Finale, Nunnally gets to deliver one to her own brother. When Lelouch tries to tell her that everything he's done has been for her sake, she flatly snaps at him, saying that she never wanted a perfect world (specially not one built on lies, war and bloodshed), as she had already been happy living with her brother. (Besides, Lelouch had already admitted to using her as an excuse to fixing the world; why he didn't admit as much, as well as the fact that he detested how things were and wanted to change them for the better, is a mystery.)
Episode 15 has Lelouch give one of these to C.C., regarding Mao and giving Geass to people knowing what can happen with it. She eventually gives Mao a Mercy Kill.
Mao also gives one to Lelouch and Suzaku.
During the chapters that focus on Team Summer A, Winter and majority of Spring living in the same village in 7 Seeds, Ango and Ryo are eventually called out on the things they had one, which included attempted rape and two attempted murders. Same characters later, thankfully, realize themselves what they did to Team Summer B and stop, although nobody else calls them out.
In Volume 8, Mrs. Akino gives one to Hakuron after the Akino's home is burned down.
Followed by one from Fuuron, who calls him out for going out of his way too much for Kurumi.
And Kurumi attempts to give him one when she recovers her memories. Doesn't work as well.
Even earlier, Kurumi gives a huge one to Hakuron when he kills Reilan.
Shizuru Fujino from Mai-HiME gets an earful from Haruka Suzushiro and Yukino Kikukawa when she essentially abandons her Student Council President post to protect Natsuki from Nao (not to mention kissing her sleeping body when no one else was around); Yukino in particular complains about her never acknowledging Haruka's efforts to surpass her, doomed as they may be, and Haruka slaps her for insulting Yukino and for being a Schoolgirl Lesbian. She takes this as a slight against both her and Natsuki, and attacks Yukino, defeating her (and killing Haruka, who was Yukino's most important person) without so much as messing up her hair; and then sets off to finish her fight against Nao.
Uryuu Ishida from Bleach gets called out by Ichigo for using Hollow bait, attracting lots of monsters, in the middle of a town filled with innocent people, all in order to have a hollow-hunt-off with Ichigo.
When Momo Hinamori attacks Gin Ichimaru in a rage, believing him to have murdered her captain, Izuru Kira, Gin's lieutenant, gives one to her while fighting her to protect his captain, calling her out on confusing public and private matters. Later on in the anime, when Rangiku visits her in her cell, she gives her another one, saying that she should have given more thought to her position as lieutenant of the fifth division, and considered how best to lead after Aizen's death.
Shortly before the Hueco Mundo arc, Tatsuki calls Ichigo out on leaving her in the dark about him being a shinigami and the situation with Orihime.
In the battle for Karakura Town, Ikkaku fights against one of Barragan's faction, and while he has bankai, he chooses not to use it to prevent himself from being forced to become a captain and leave Kenpachi's service. As a result, the strategically important pillar he is protecting is destroyed, and Iba calls him out on disobeying orders for his own desires.
A heartbreaking one occurs in Chapter 453 when Tatsuki calls out Ichigo for tossing Tsukishima into a window, after he had brainwashed Ichigo's family and friends into believing he is their cousin/friend. What makes it worse was that Ichigo was trying to protect them and they think he's losing his mind.
The Prince of Tennis's Akaya Kirihara, a child-like and cheerful guy who turns into a Tyke Bomb when in the courts, is the first one to get called out. One of the managers, An Tachibana, is the younger sister of a player he seriously injured with his violent tennis style; at some point she corners him to talk about that, but a verbal fight ensues, since Kirihara himself resorted to insulting her and her brother's team.
The second one is An herself. After her fight with Kirihara and with him injured after falling down a flight of stairs, which could've ended in Death by Falling Over, An understandably panics and pretends to not know anything, so someone else is blamed by the others - Akira Kamio, An's Unlucky Childhood Friend. Ryoma unmasks her, and Kamio reprehends An for her conduct because, as angry as Kamio himself is, he wouldn't deliberately resort to violence. (As for Kirihara himself, he has kept his trap shut because he doesn't want even more problems for An and himself.)
And the third is Ryoma Echizen. He had been acting uninterested and bratty all the while, ignoring the challenge posed by a certain boy named Kevin Smith...until he sees Kevin play. Ryoma then practically demands to be in the Senbatsu team, which is seen by sub-coach (and Seigaku captain) Tezuka as a very rude request because Ryoma is putting his personal desire over the team's needs (seen as a huge insult to the team). Tezuka is actually so upset that he slaps Ryoma in public. Ryoma has to go into Pose of Supplication to regain Tezuka's trust..
Haruhi Suzumiya: Kyon often calls the series eponymous character on her more sociopathic antics. Normally she just ignores him and even when she does back down she never concedes that she was over the line. But when she got Mikuru drunk and attempted to make Koizumi take her first kiss while she was out of it just for the sake of her student movie and followed it up by insisting she could do that because Mikuru is her toy, Kyon was so furious that he actually tried to hit her. Fortunately both Koizumi and Mikuru stopped him or the world would probably have exploded.
In the books, he also calls out adult Mikuru on her mistreatment of her past self.
Kyon has a conversation with himself in the Disappearance movie that essentially applies this trope to himself. His mind asks him why he's complaining about all of Haruhi's hijinks that he finds himself dragged into, yet when he's suddenly in a perfectly normal world, he doesn't like it either. He then asks which world he'd really rather belong in, and gives a rather awesome and heartwarming answer.
Subverted for the majority of Berserk. In the first story arc, Guts lets himself get captured by some soldiers after killing a couple of bandits, knowing full well that the bandit leader will destroy the town he's in to kill him. When Puck calls him out on this, Guts laughs it off and replies that if the townspeople can't defend themselves, then they deserve to die. Throughout the series, Puck reprimands Guts for his actions, but the trope is averted because Guts couldn't care less about Puck's feelings and is never presented as a good guy to begin with.
However, this all comes tumbling down at the beginning of the Conviction Arc. Before the above events happened, and after the tragic Eclipse, Guts left his maddened girlfriend Casca in the hands of Godo, an aged blacksmith with a small daughter Erica, and Rickert, a young boy and the only other surviving member of the Hawks. He then left to hunt Apostles and the Godhand and returned two years later only to learn Casca wandered away from Erica in the woods and is now missing. Guts flew into a rage and started yelling at Rickert for losing her and for not being out looking for her. Erica tearfully told Guts he all but disappeared on them for two years and that Rickert did go looking for her but returned to support them as Godo's been seriously ill. Godo, dying of old age, pointed out that Guts himself abandoned her in his own rage and as such he had no right yelling at Rickert. He also noted that Guts had allowed hate and anger to consume him in his grief over the Eclipse. This is the first time that the What the Hell, Hero? lecture is played straight in Berserk, as it causes Guts to make the protection of Casca his top priority and he begins to revert to how he was before the Eclipse. Even Puck is surprised that Guts' entire attitude changed when it came to saving one woman.
In Mirai Nikki, Yukiteru calls Yuno on her claim that she locked and chained him up in her room and tried to kill his friends because she loved him. To put it in his words: "What the hell?!"
In Fullmetal Alchemist, several of Roy Mustang's colleagues, particularly Ed and Armstrong, have this reaction when Roy kills Maria Ross by burning her alive because she's suspected of killing his friend Hughes. Turns out Roy actually faked Ross's death and smuggled her to Xing to protect her.
Later, Ed, Riza and Scar give him one when he's prepared to finish off Envy in revenge for killing Hughes, and Riza even threatens to fulfill his request to shoot him - and herself after the battle is over- if he strays from his ideals.
Also, Ed has one of these moments with Ling after the prince willingly lets himself become a homunculus. While the second Greed wasn't exactly a hero, he still got one from Ling when he killed one of the chimera who had worked with the first Greed and who was only looking for his old master.
In YuYu Hakusho, Kuwabara gives one to Yusuke, Hiei and Kurama when they go off to the Demon Plane in the Three Kings arc, claiming that they are no better than the demons they fight in their seeking battle.
This wasn't the first time Kuwabara gave one of these. During the Dark Tournament saga, he was the only one of the main fighters to be left in the dark about Genkai's death via Younger Toguro, and only found out about it when Elder Toguro boasted about it during their match. After the fight and his initial horror has worn off, Kuwabara expresses how angry he is with his teammates for leaving him out of the loop. By punching Yusuke in the face.
Kuwabara: I thought we were a team, but I guess I'm just one big joke to you all, aren't I? Well, this joke has feelings! Genkai meant a lot to me, too! (grabs Yusuke by the collar) Did you all just sit around about how clueless I was?! Is this how you get your kicks, Urameshi?! Answer me!
In the beginning of the Three Kings Arc, Yusuke meets with some demons who serve his ancestor Raizen, and reveal that a three-way conflict has ensued between them over whether eating humans is forbidden, an unpleasant necessity or entirely permissible. Yusuke says that to the demons, this must be a mere argument over the food supply. After the demons depart, former Spirit Detective Kuroko Sanada walks up to Yusuke, having heard the conversation, and says that in light of what she heard, she's deeply uncomfortable with what he has become.
Kuroko: "You should go to the Demon World. In fact that's probably the best thing for everyone. After looking a demon who's eaten humans in the eye and distinctly referring to those humans as a 'food supply', I don't think you belong in the Human World anymore."
Dragon Ball Z: The final battle with Cell. As Gohan's busy getting beaten to death by Cell (with Goku and the others just standing there watching), Goku wonders out loud what Gohan is waiting for, expecting the fight to bring out Gohan's full power. Team Dad Piccolo (who, frankly, was more of a father to Gohan than Goku was to that point), disgustedly calls out Goku for healing Cell and then just standing there watching him pound the life out of his son. Piccolo points out (correctly) that Gohan wasn't like him or Goku or Vegeta: he didn't revel in the fight; he was just wondering why his own father was just watching him get beat to death, wondering if his father values a fair, manly fight more than his own son's life, and that, even though it would probably cost him his life, he was going to jump in and help. Cue the "Oh, Crap! My God, What Have I Done??" reaction from Goku. Here's the original speech Piccolo gave to Goku in all it's scathing glory:
Goku, you're mistaken... Gohan isn't a fighter like you. Does Gohan know about your plan? Did you even talk to him about it before the Cell Games? Do you want to know what Gohan is thinking right now!? He isn't thinking about anger he's thinking 'Why isn't my father coming to rescue me from pain and death!? My father seems to value a fair manly fight more than my own life.' Never forget that even though he may be the strongest of all of us, he's still a child!! I'd rather die than wait!
Krillin also calls Goku out for letting Vegeta escape after he's facilitated the deaths of their friends and beaten the living hell out of them. Goku just smiles and says he wants to fight Vegeta again. Granted, Vegeta turns into a valuable ally and Krillin pulls a similar trick two arcs later on his future wife, Android 18.
Deconstructed while being Played for Laughs when Ox-King tells off Chi-chi for berating Goku in letting Gohan fight over having Gohan continue studying. At that point, Gohan has surpassed Goku and Cell in strength having transformed into a Super Saiyan 2 and can now beat Cell. Chi-chi of course takes this the wrong way and proceeds to Calling the Old Man Out while throwing an even bigger hissy fit.
Bulma also delivers one to essentially the whole Z-Gang for being so fight-obsessed that despite Trunks coming all the way from The Future to tell them about how much of a Crap Sack World things'll be due to two renegade androids and giving them three years of prep time, Goku, Tenshinhan and especially Vegeta essentially say "That's too easy, we'll just train until they arrive, cause enough damage to get noticed and when it's all over, we'll just use the Dragon Balls to revive everyone!" No wonder Old Kai called them on their reliance on using the dragonballs so often when the audience initially thinks he's just a cranky old geezer for blaming Bulma for making the Dragon Radar.
Bulma calls the remaining Z-fighters out after it seems that Goten and Trunks have been defeated by Buu and Piccolo had destroyed the door to the Time Chamber to stop him escaping, trapping them in there forever. When Krillin cheerily states that Piccolo can just kill them and himself, then bring them back to life with the Dragonballs, Bulma goes ballistic, and tears the rest of the Z-Fighters a new one.
Bulma: Are you even listening to yourself?! Relax, because they're trapped with a monster that could kill them!? They were children! They should have never been made to fight! You grown men left the fate of the Earth in their hands! I hope you're ashamed!
The original version of that speech is even more brutal. Bulma pulls no punches and flat out calls the rest of the Z-Fighters cowards!
After Gotenks got absolutely pummeled by Majin Buu and returns to Kami's Lookout, Piccolo chews the hell out of Gotenks for charging at Majin Buu without coming up with a proper strategy or at least listening to his suggestions. Then when Piccolo destroyed the only exit to the Hyperbolic Time Chamber Gotenks goes nuts at Piccolo for doing so as he claims he still had secret technique that could have killed Majin Buu even though he previously stated he had no strength left and his powers reached his limits. Piccolo then yells back at him for putting the world at risk just to put on more of a spectacle of a battle.
Bulma was one thing. Vegeta gets pissed at Goku for leaving behind Gohan, Goten, Trunks, and Piccolo behind on Earth to die when Buu destroyed the planet, instead escaping with just themselves, Dende, Bee the Dog, and Hercule. Although it's likely that Goku and Vegeta would never have been able to reach the quartet before getting caught in Buu's blast, the insult still hurts, and is entirely understandable.
Vegeta: And what do we have here? (grabs Goku by the collar) Urgh! Idiot! How could you?! You saved the Namek boy and that big oaf instead of your own sons?!?! HAVE YOU LOST YOUR MIND?!?!
Goku: (looks away, ashamed)
Dende: (meekly, with his head down) Vegeta... sorry.
In One Piece Hannyabal points out that Impel Down is one of the things keeping the world safe, and Luffy causing a mass breakout would cause mass panic. Luffy simply doesn't give a crap about things like that.
To be perfectly fair, even then, Luffy drew the line at freeing Crocodile. Not even he could overlook what he had done, and he wouldn't have freed him if it wasn't for Emporio Ivankov.
During Luffy's argument with Usopp, Luffy is about to suggest that if Usopp is so dissatisfied with his decision, he should leave the crew. Sanji kicks Luffy into a wall, angrily telling him to think before he speaks. Luffy apologizes, but the damage is done, and Usopp, convinced that Luffy is throwing away useless crew members, announces his intention to leave.
That whole sub-plot is resolved with another What the Hell, Hero? moment, when, while the others (including Luffy) are discussing Usopp rejoining the crew as if it were a matter of course, Zoro points out that Usopp left the crew willingly in deliberate defiance of Luffy, and said that if Luffy was so spineless to let Usopp back in without making him apologize, then he (Zoro) would leave the crew.
In the Drum Island arc, during a tense standoff between the village guards and the Straw Hats, someone fires a shot and Vivi’s shoulder is grazed. Luffy gets angry and it seems as though a fight will break out, but Vivi enters a Pose of Supplication, begging the villagers to let them in, and chastises Luffy for losing control, saying that he’s “not fit to be (their) captain”. Luffy gets the hint, apologizes and follows suit with Vivi, prompting the villagers to let them in.
When they reach Fishman Island, Sanji gives such a speech to Jinbei involving the latter's past relation with Arlong.
Parodied when Sanji finds out that Luffy spent the 2 year timeskip on an island full of women while he was stuck on an island full of Okama. To be fair, neither found the experience pleasant (Luffy had no interest in the women; he just wanted to get stronger).
But the mother of all examples is when Koby finally speaks out at the end of the Paramount War, when the violence is continuing even after Whitebeard and Ace are dead:
"THAT'S ENOUGH!! Let's stop this!! Stop fighting!! It's a waste of human life!! (Each and every soldier...has a family waiting for him at home!!) We've achieved our objective!! We've broken the pirates' power!! So why are we chasing them?! It's not necessary!! This is pure bloodlust!! Some of the wounded can be saved if they're treated right away!! But we're consigning them to death and creating more casualities to boot!! The soldiers who die from here on are...they're just...just... They're fools who will die for nothing!!"
Sengoku, despite being a Well-Intentioned Extremist, was rightly pissed off when the World Government decided to cover up the breakout of several Level Six prisoners from Impel Down, in order to save their reputation. After the bullshit he's gone through the last few months, along with the rest he's probably gone through his entire tenure as Fleet Admiral, this was the last straw. He retired soon after.
And don't forget Dadan's verbal and physical beatdown of Garp following his return to Luffy's hometown.
In Pokémon Special, Ruby participated in a Pokemon Contest despite the fact that the world was in danger, only to lose to someone he greatly admired. He blamed his Feebas for the loss, which caused her to run away in grief. While Ruby got better after the initial tragedy of taking his frustrations and failings out on his teammate, Wallace has to spell it out to him first.
Here is the speech:
Wallace: I don't know what happened at Fortree, but venting your anger out on your Pokemon is inexcusable! What's more, you blamed your Pokemon for your own mistakes as a Trainer. That's unforgivable! And before you turn on me or argue about the loss of the contest...isn't there something you should be doing right now?
A Played for Laughs variant happened in the Yellow arc, when Sabrina learns that after she had gone out of her way to protect Blue from Lorelei after they were cuffed together, Blue wasn't really chained to her at all and the two could have seperated their arms any time.) Blue justifies this by saying that she needed to fool Sabrina to effectively fool Lorelei.
Blue: So you forgive me, right? Sabrina: DON'T HOLD YOUR BREATH.
In Yu-Gi-Oh!, after Yami's use of the seal of Orichalcos results in Yugi losing his soul, Yugi's self-proclaimed girlfriend Rebecca chews him out for this, saying that if he really were noble he would never have done something that horrible. Yami doesn't even try to defend his actions there.
Note that the above example only happens in the 4Kids dub. In the original version of that episode, Mai was chewing out Yugi for being so focused on Pegasus that he wasn't paying attention to her or their duel; the whole "fear of what Yami might do" sub-plot wasn't in the original at all, but was added to the dub.
The abridged version of the tenth anniversary movie had all three series protagonists chew out Paradox for his harsh methods in averting a Bad Future.
An odd example happens in the third season of Yu-Gi-Oh! GX. Yubel spends the whole time blaming Judai for abandoning her, claiming that what happened to her is his fault. What's odd about this? Judai eventually realizes that she's right. In fact, he decides to make amends, taking full responsibility for Yubel by bonding her soul to his.
In Naruto, Yamato informs Naruto about his injuring Sakura while in four-tails mode, and tells him that if he wishes to bring Sasuke back, he should rely on his own power to do so and avoid becoming agitated enough to go into fox mode. Yamato and Kakashi lecture him again after one of his Leeroy Jenkins moments in the Three Tails arc, saying that it put himself and his comrades in danger, but both concede that Sakura's dropping down on Naruto and punching him into the ground was much more effective.
Then there's Sakura's (fake) confession to Naruto. In her attempt to stop him from chasing after Sasuke and hurting himself, she wasn't very convincing and caused Naruto to call her out for lying to herself and to him.
Asuma, Ino, Shikamaru and Choza all get angry with Choji when he puts himself and his team mates in danger by refusing to attack Asuma, who has been resurrected via Edo Tensei.
Temari and Shikaku both call Shikamaru out in the Rescue Sasuke arc when he considers giving up being a shinobi. Shikaku, in particular, is furious with Shikamaru and calls him a spineless coward, adding that if he drops out of being a shinobi, his team mates will only go off with someone else and possibly be killed, and he has the chance to prevent that happening.
Naruto gets called out by Itachi on his insistence on trying to do everything by himself. Itachi tells him that doing so is disrespectful to the people that care about him, and it's egotistical of Naruto to think that he can solve all the world's problems by himself. Of course, later chapters reveal that Itachi did the same, thus he knows exactly that Naruto shouldn't make this kind of mistake.
Subverted in JoJo's Bizarre Adventure, wherein Jotaro was part of a high-stakes poker with the devious gambler D'arby, the betting collateral his soul and the souls of Polnareff and Jotaro's grandfather Joseph on the line. Avdol was perfectly fine with Jotaro adding his own soul, believing in him so you would. Cue the horrified calling out when Jotaro decides to add both the souls of the then-hospitalized Noriaki Kakyoin and HIS OWN MOTHER to the pot. Of course, this was all a clever Batman Gambit on Jotaro's part designed to wear D'arby down mentally, to the point where D'arby would subconsciously admit defeat, freeing the souls of those he had beaten (Via cheating but still). Earlier still, Avdol called Jotaro out for using Star Platinum to break D'arby's finger...until Jotaro himself called out D'arby's attempted slight of hand trick.
In the manga Sailor Moon feels much the same way towards them for immediately jumping to kill Hotaru rather than find a less...murderous way to settle things. They appear a good bit more sympathetic later, when it's revealed that they just don't want the world to end like it did before and they didn't know that after Saturn destroyed everything in the world then Sailor Moon would use the Silver Crystal to revive all the good things.
In the SuperS special, a villain calls out Michiru for destroying a potentially-apocalyptic vase in order to save Haruka, pointing out that she had no idea she wasn't ending the world. Michiru calmly let the villain know that there was no point in a world without Haruka, implying that she valued her girlfriend more than the safety of the world.
In Sailor Moon R, Usagi does this to Chibi-Usa, coming close to beating the girl after the latter foolishly stole Usagi's brooch in an attempt to take her Silver Crystal back to the future, leading to the other Sailors to get captured by Rubeus when they tried to interfere and save her. Mamoru has to hold Usagi back from doing so
Legend of Galactic Heroes: Kircheis issues Reinhard a What the Hell, Hero? for not stopping an enemy attack that wiped out an entire planet of innocent civilians (note in the anime version, Reinhard only agreed to consider not intervening, believing he had more time to think about it than he actually did). Years later, after Reinhard becomes Emperor, a man whose family was killed in the attack calls him out in public, accusing him of building his empire on the corpses of innocent women and children.
In the manga adaptation of Battle Royale, Yutaka gives Shinji a hell of a one of these after he accidentally-on-purpose shoots Keita in the face.
The task force call L on several of his actions in Death Note — both the genuinely extreme ones (torturing Misa to the point of almost insanity) and the ones that are probably just pragmatic (trying to let Higuchi continue to kill so that L can determine his method of killing.)
The task force calls Near out for having Misa and Mogi abducted as a precaution, saying that doing so is illegal. However, Mogi reveals that they consented to this.
In one episode of Speed Racer, an opponent needs to win to get medicine to save a loved one, yet the title character won't lose on purpose because that is "cheating", despite protests from Trixie. Fortunately she sabotaged him, putting people ahead of the integrity of the race.
In Ouran High School Host Club, Kyouya calls out Tamaki's father Yuzuru for his plot to get Tamaki's grandmother Shizu removed from her position as president of the Suou family business. Yuzuru intended his plan to remove his mother's control over the family so that he, Tamaki, and Tamaki's Missing Mom Anne-Sophie could be together as a happy family... but Kyouya correctly points out that he had no understanding of Tamaki's own feelings on the subject and simply used him as a pawn, dashing Tamaki's dreams of having all of them together as a family in the process.
In the backstory of Seirei no Moribito, normally laid-back and patient healer Tanda called Balsa out over how many people she was killing while working as a bodyguard, asking her how much meaning her vow to save eight lives could possibly have if she was killing so many others to do it. Some two years later, he admits that it came as much out of his fears for her safety and his unrequited love for her as anything else, but Balsa took it to heart nonetheless.
In the Bokurano anime, when Youko is outed as The Mole by Kirie in his last breath, Anko gets so pissed off at her that she repeatedly slaps her around, screaming about how she's to blame for all the heartbreak that the kids have gone through as things get worse and worse.
Also in the anime, when Daichi, who raises his siblings on his own after his father's departure is uncomfortable about being chosen as the pilot, which will result in his own death, Ushiro accuses him of getting cold feet and not meaning what he said earlier about wanting to do the right thing. Tanaka, however, responds with "Ushiro-kun, that's enough. Everyone's scared." Considering that he's her son, that comment has considerably more weight.
In the third anime series of Slayers, it's Filia's turn to be called out; even after it's been spelled out to her that the emotionally traumatized Big Bad is beyond salvation, she refuses to have him destroyed out of guilt, which in itself she didn't gain until it is plainly spelled out to her that her race of dragons ended the main villain's out of paranoia.
In Mahou Sensei Negima!, Chao essentially calls the collective presence of mages living on Earth, pointing out that it's really unethical for them to hide all of their abilities from the rest of the world, especially when a lot of magic is pretty freaking dangerous. Notably, the protagonist admits that she has a point and almost joins her, but ultimately opposes her anyway because while he agrees with her in theory, her methods cause way too much collateral damage for him to be willing to switch sides.
There was a lighter one in chapter 349, where Yotsuba calls out the girls who were trying to force Negi to confess who he likes. Her rationale? He's only ten, they already know about his magic and parentage, several of them have patios with him and he's busy with trying to save the world. Is he not allowed to have any secrets at all?
In Bakuman。, the main characters get this after they submit a one-shot manga to a Treasure contest that Eiji Nizuma is judging, thus violating the rules of their contract, and Hattori tells them to consider Miura’s situation.
In Panty & Stocking with Garterbelt, Garterbelt constantly berates the angels for their selfish and irresponsible behavior. It never works. In episode 13, Brief of all people snaps and calls them out on their callous reaction to Garterbelt's apparent death.
In Gundam 00 Season 2, Saji Crossroad runs from the Kataron base and ends up captured by the military. In order to make it very clear that he had nothing to do with the rebels, he spills out their location, which resulted in a mass killing. Tieria then hits him and lectures him because of his selfishness.
Eikichi Onizuka in Great Teacher Onizuka often goes to extreme lengths to teach his students (and other teachers) a simple life lesson. These invariably get him into some kind of trouble when the higher-ups find out.
In a few instances his students and his friends have called him out on his less noble decisions. For example, Ryuji refuses to talk to him after he starts kissing up to Ms. Daimon and her "points" system, rather than being genuinely concerned with helping his students.
Soul Eater: The eponymous character, having taken a level in maturity, calls Black★Star out for his stubbornness. Namely, not recognizing the consequences that could result in telling Cute Witch Angela about Mifune's death.
In Muhyo And Roji, Muhyo calls out Roji for going alone with Nana to deal with a haunt and failing to bind it with his ward, saying he almost got her killed. Roji earlier tries to give Muhyo one when he thinks he's sending Nana's father's ghost to Hell, but relents when he finds out that he's sending the ghost to the Styx (essentially Purgatory).
Shouma Takakura from Mawaru-Penguindrum does this twice: once to Ringo (after her Attempted Rape of Tabuki) and later to Kanba (after finding out his illegal deals to save Himari's life) The first one works, as Ringo has a change of heart few afterwards (though it takes Shouma suffering body harm for her) the second fails horribly since Kanba has already gone Knight Templar Big Brother, thus he beats Shouma up and then leaves the family..
In Tengen Toppa Gurren Lagann after the Time Skip, during the Anti-Spiral's first attack Simon immediately rashly rushes out to counterattack them, but his lack of having a proper plan in dealing with this new enemy nearly causes an entire city's population to get killed because of this. Although he had no way of knowing this. Rossiu proceeds to call him out on it.
Rossiu himself is called out by the chief of legal affairs when he orders Simon's execution.
This is what quite a few side characters in Superior think they're doing when they tell Exa about all the people who will die if he doesn't kill monsters like he's supposed to. Given that Exa thinks monsters are people too, he has issues with their arguments. (When he actually gives in at one point, a character who just a few chapters ago had been criticizing his beliefs instead calls him out on not living up to the pacifistic ideals he keeps promoting.)
In Dragon Pink, the protagonists encounter a group of "Slave Knights" - skeleton warriors who each have a naked girl captive in their ribcage as a Human Shield. The protagonists make an offhanded apology and immediately tear into one knight, brutally killing the girl. The rest of the knights are horrified by this behavior from a human.
In Tenchi Muyo!, Tenchi calls out his dad and grandpa after finding out that his mother wasn't the kindly woman he remembered, but a prankster that even made her death into a joke and they went along with it as part of her last wish.
In Science Ninja Team Gatchaman, G-1 goes on a Roaring Rampage of Revenge after Berg Katse's plans result in the death of his father. This leads to him: torturing a prisoner (by beating him and spraying him in the face with a fire extinguisher); being too ready to believe that prisoner's confession of the location of Galactor Headquarters (it was just a base); and leading his teammates into a death trap. G-1 tries to justify himself by telling them he swore he'd avenge his father. G-3 proceeds to verbally kick his arse, pointing out that the five of them are a team, that all but one of them have lost their own fathers, and G-1 is being a jerk putting his desires over the team he commands.
In Black Lagoon, this is what Fabiola says to Revy after the latter summarily executes a wounded FARC fighter who they told that they would take to the hospital if he gave them information. She also gives one to Rock at the end of the "El Baile de la Muerte" arc, because of him using most of the characters involved as pawns and the fact that he did it for fun as well to win the bet with Mr. Chang.
When Jin asks Sorata about his leaving Sakura Hall at some point in episode 3, Sorata gives him the runaround. He then also asks about Mashiro, and that if Sorata was so tired of it, he would take over "Mashiro duty" (i.e. being her Cloudcuckoolander's Minder) as well as the cats, so that Sorata could then be free to leave. Jin tells him that because he's sick of Sorata's lack of commitment regarding working towards a goal, as evidenced by his runaround answers.
In Episode 10, after Rita explains how she failed to meet expectations due to being overshadowed by Mashiro, Ryuunosuke calls her out on trying to appease others' expectations of her more than following her true desire.
Chuunibyou Demo Koi ga Shitai!, anime edition: Sanae gives a rather heartbreaking one to Yuuta after he lets Rikka leave to go see her father's grave in episode 11, telling him that Rikka had been waiting for him to call Rikka out on her total rejection of her chuuni persona and blaming him for her sudden change.
In the Pokémon episode "Piplup, Up, and Away!", the Team Rocket trio of all people call out Ash, Dawn, and Brock on not noticing how miserable Piplup was.
In an Advanced Challenge episode, Nurse Joy of all people hammers into May a big one about how she was pushing her Bulbasaur too hard.
In the Pokémon Advanced episode "Brave the Wave", Ash was annoyed because he lose the battle against a carefree Gym Leader. Then he is called out by Nurse Joy, May, Max, Brock and even Pikachu for forcing his Treecko to fight beyond its capabilities during said battle. His reaction? Instead of taking his friends' advice like usual, he clamis that they know nothing, and then he lashes out at Brock by yelling a big "Shut up!".
During and episode of The Johto Journeys, Ash calls out Casey for her not caring about all the pain her Chikorita is going through during the bug catching contest.
In an episode of Master Quest, a girl training her Pokémon hard for cheerleading yells at her Pokémon for failing a move; in fact, when they start crying from shame, she only yells at them more. Misty then quickly calls her out for caring more about winning than her own Pokémon and not even bothering to check and see if they were all right. That's when the girl, after recalling the times she cared for her runaway Politoed, tearfully apologizes to her Pokémon, and they accept the apology without question.
In Girls und Panzer, Miho, having transferred to Oarai to avoid doing tankery, is quite upset when she hears that it's being offered again this year, and decides not to take it. The student council then calls her into their office, and Anzu, the president, says that if Miho doesn't take tankery, she won't be attending next year. Saori and Hana, Miho's new friends, are outraged over Anzu's pressuring Miho(even if it turns out to be so that Oarai won't get shut down), having noticed how uncomfortable Miho is around tankery, resulting in an argument that only ends when Miho decides to take tankery to be with the friends who supported her.
In Little Army, Miho's friend Emi dislikes Miho's older sister Maho from the moment they first meet, causing some friction between Emi and Miho, as it's thought to be because Maho's team defeated Emi's older sister's team. Finally, Emi admits the real reason she doesn't like Maho; Maho, during the last tournament, shot the enemy team's flag tank (an instant win condition) when it went to rescue one of the tanks on her team during an emergency, even though she could have won anyway. Miho is quite shocked to hear what Emi said is true.
In the early episodes of Initial D, Itsuki often yells "TAKUMI YOU IDIOT!!"
Athrun and Kira both do this to each other in Gundam Seed Destiny. Athrun pointing out the Kira is interfering in Zaft operations, while Kira counters he won't trust Zaft because they sent assassins after them and are using a fake Lacus Clyne to use her influence for their own agendas and yet Athrun is seemingly ok with this. Athrun counters he'd never heard of assassins and Kira has no proof it was Durandal. Later on he tries this again in battle and Kira again counters that no matter how Athrun tries to justify himself he's still fighting against them, and therefore is their enemy. At this Athrun breaks, leaving himself unable to resist Kira's disabling blow. And since Kira's distrust is later proven right, when Durandal tries to kill Athrun for not agreeing with his plans he eventually agrees with Kira and admits he choose poorly, although Kira also admits he might have been a little too harsh.
Athrun tries this with Shinn too regarding his bloodlust and willingness to slaughter anyone deemed an enemy, but Shinn who has a massive chip on his shoulder due to events in his past, refuses to believe he's doing anything wrong.
In Fate/Zero, Emiya Kiritsugu correctly predicts this from Saber due to her nature. He arranges for his wife Iris to accompany Saber as her Master so he can operate with as little contact with her as possible. Eventually both Saber and Lancer get opportunities to lecture him.
Kiritsugu lectures Saber right back, saying that her code of "chivalry" has a way of glorifying combat, and therefore perpetuating war. In his mind, there is nothing good or honorable about war... so the correct path should be to end it as swiftly as possible, regardless of the method used. Saber is obviously disturbed and disagrees, as his murdering was utterly pointless in her eyes.
In HeartCatch Pretty Cure!, Yuri snaps at Itsuki for allowing baby fairy Potpourri to run off like he did, though Itsuki understands why it happened.
Near the end of the series, Coffret snaps at Erika for her blatant misuse of her powers. When she passes out asleep and leaves the Marine Tact out, he snatches up and run off as a punishment to her.
In Attack on Titan, Eren is called out by Mikasa and Armin due to his unwillingness to fight Annie/the Female Titan, despite the fact she killed Levi's personal squad and several other soldiers.
Jean of all people points out how Mikasa's protectiveness over Eren affects her normally rational thinking and causes her to become suicidally reckless when he is in danger. Eren himself called her out early in the series for caring more about him than the human race.
In Magical Record Lyrical Nanoha Force, Tohma gets scolded several times by Reinforce Zwei and Isis, due to his over-friendly personality toward the Huckebein, who, circumstances aside, are still a bunch of unrepentant mass murderers.
In Date A Live, Shido Itsuki calls out Origami Tobiichi and her organization AST for their "shoot on sight" policy in dealing with Spirits. Sure, Spirits cause a lot of destruction, but they never considered alternate methods in dealing with them, and never even try talking to them. Most Spirits are just scared girls who don't realize their powers can wreck everything.
In Campione!, Godou Kusanagi is constantly called out for his I Just Want to Be Normal attitude and extreme reluctance to fight. When he shirks his God-slaying responsibilities, people will get hurt.
Kyoshiro from Ginga Densetsu Weed calls out Weed for banishing Jerome from the pack when the latter kills the assassins Thunder and Lector. Weed, however, sticks to his decision, and Kyoshiro decides to split his pack from the Ohu dogs.
After saving Tsukune from Tamao and the Swimming Club mermaids, Inner Moka promptly bitch-slaps Tsukune and chews him out for getting in the water with Tamao in the first place, especially since seeing him do so really hurt Outer Moka's feelings.
When the StudentPolice have Tsukune arrested and scheduled for execution, Headmaster Mikogami explicitly says that he's not going to stop Kuyou from doing so and forbids Ms. Nekonome from doing the same; Ms. Nekonome wastes no time in calling him out on his decision not to act, especially since Yokai Academy's entire purpose is to support co-existence between humans and monsters. Considering Mikogami's Chessmaster status, he could easily have been setting Tsukune and his Unwanted Harem up to take the Student Police down; still a pretty douche move, though.