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.
Nunnally calls out Suzaku: she gives off a very disturbed expression when she hears Suzaku call Kallen by her prisoner number when he requests to interrogate her, and in the following episode, after being refused in her requests to Suzaku to touch his hand to know if he is telling the truth or be assured that her brother Lelouch is safe, she calls him out for being a liar.
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 the most notorious Britannian royal sibling, Schneizel, who launch a nuke at their own country, almost immediately). The result is that he loses his entire army.
In the Grand Finale, Nunnally gets to deliver the best What the Hell, Hero? comeback of the series. 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.
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.
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 Yu Yu 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.
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. The anime is a bit easier on Goku than the manga — mostly due to Goku's expression being changed from "Dull Surprise" in the manga to more "Oh Crap! My God, What Have I Done??"
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.
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 Dragonballs 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 also 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, saying: "They were children, they weren't even meant to fight! You grown men stood back and let this happen!"
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 ere on are...they're just...just... They're fools who will die for nothing!!"
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.
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.
Also, during Yugi's duel with Mai, he refuses to let Yami take over. When Yami asks why, Yugi tells him it's because he fears he'll try to hurt Mai if needed to win, since he was ready to ''kill'' Kaiba before, by winning when Kaiba was ready to commit suicide when he pulled a cruel Batman Gambit to beat him at the gates of Pegasus's castle. It takes Yami pretty much pleading with him and Mai chewing Yugi out herself to have him change his mind.
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 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.
Not that Itachi himself has room to talk. A lot of that statement seems to have been Itachi giving it to himself as well for trying to shoulder every burden. He couldn't have made it worse if he tried. Not only did he destroy Sasuke's emotional stability, he nearly got many good people killed, helped Akatsuki and messed up everything he touched. This trope applies to him hard. Also, Naruto had a justification: he wasn't in full control of the power of the beast within him and was worried about what would happen if he lost control. As shown in his battle with Pain, he probably had a point. In the anime, Itachi ended his speech by saying "I tried to do everything by myself and I failed." He was just trying to keep Naruto from repeating his mistakes.
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 Black Butler, Ciel Phantomhive, the Troubled, but Cute hero, has gotten one of these from, of all people, Sebastian, his demonic butler. In Chapter 34, his Stalker with a Crush takes him down to the basement to show off a room that is an exact replica of the room where Ciel had nearly died as a sacrifice for a bunch of cultists to summon Sebastian in the first place. Ciel has what is his first shown full-out episode, and he kills the stalker upon his request. After this, Ciel proceeds to tell the orphan who has worked with the stalker to help his brothers and sisters that he did not do anything wrong by killing those children because he was protecting those he cared about, and needed to start giving a damn about himself. Then comes the Doctor, who reveals that he was making sure the children's corpses aren't reaching the cemetery by using their bones to create prosthetic limbs. Ciel reacts violently, insisting that Sebastian kill both aforementioned orphan and the mad doctor. Afterwards, Ciel demands they burn down the mansion, with the kids still inside. Sebastian then reminds Ciel that their job was to save the kids in the first place. Unfortunately, Sebastian is bound to Ciel's will, so has to obey him.
Sailor Moon S has Haruka and Michiru calling out Usagi for being too soft on Hotaru, the local Apocalypse Maiden.
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.
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.
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 the Neo HK arc of G Gundam, Domon snaps when Allenby is kidnapped when she's under Rain's care and chews her out rather harshly. When Rain has an Heroic BSOD and resigns from the Neo-Japanese team because she thinks of herself as a failure to their mission, Domon is told by Dr. Mikamura that he's full of shit.
Domon: "Leave of absence? How can she be so selfish?!"
Dr. Mikamura: "You fool, you are the selfish one! Rain has always had a strong sense of responsibility, you pressured her until she snapped. That's why the Kasshus can't fully be trusted!"
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.
Generally Played for Laughs in Full Metal Panic, with Kaname chewing out Sosuke for one of his plans. Played for drama at the end of the Second Raid, when some soldiers call out Sosuke on his Heroic BSOD, and the fact that he seems about ready to start killing everyone. Kaname snaps him out of it.
In the finale of Ghost in the Shell: SAC: 1st GIG, the Umibozu repeatedly call out Section 9 for killing them while resisting arrest, especially when Batou executes one that he'd just Mind Controlled.
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. Rossiu proceeds to call him out on it. Although never directly stated, it also likely contributes to Rossiu's decision to make Simon the scapegoat for allowing the Anti-Spiral to destroy the world —- since he's already clearly screwed up royally once, why not make him the fall guy for everything?
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.
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.
In Heartcatch Pretty Cure, Yuri tells Itsuki off for letting the young fairy Potpourri run off on its own, mostly because she had no idea how to handle one when dealing with school. It's also a hint as to why Yuri's in the state that she is in - because she couldn't protect her own partner, it died.
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 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.
