The Adventures of Baron Munchausen: Used as setup for some Rule of Funny. The Baron has decided to save Sally's village but to do that he must first find his old trusty companions. The first one encountered is Berthold who was trapped in a parrot cage by the King of the Moon over a rather long span of time and has consequently come down with a rather bad case of Trauma-Induced Amnesia.... It wears off a little later however and:
Berthold: Hang on. Hang on! It's all coming back. I've-I've been stuck here for over twenty years, ever since you were last here on the moon. You abandoned me here! You swine! You toddled off with that old queen of tarts and left me to rot in that parrot cage, didn't you? And now you come back here, just because it suits you, after wasting half my life and expect me to follow you to the ends of the earth! Baron:Yes. [beat] Berthold:Oh, all right.
The Avengers: This is the reaction Captain America has towards Nick Fury upon learning that SHIELD had been reverse-engineering weapons and tech from confiscated HYDRA weaponry.
Babylon AD: In one scene, when the protagonists are attacked, a wrestler (motivated mostly because of an attraction to Aurora) steps in and helps them. Right after the thugs are taken out, Vin Diesel savagely beats and murders the wrestler for no reason other than to be a dick. Aurora calls him out on it, "He was trying to protect me!" However, Vin did it because he was trapped in a cage with a punch-drunk boxer.
Bad Education: This is Enrique's reaction in learning that Juan helped Father Manolo to murder his brother Ignacio.
The Bad News Bears: Team manager Buttermaker gets a couple of the these. The first comes from the bulk of the team when he revealed that he told star player Kelly to catch every ball he could get to (even if it should have been someone else's play) in order to make the championship. During the championship game, he gets it from team nerd Oglevie about allowing Amanda to continue pitching with a tired arm.
The Bank: The protagonist Jim Doyle lies in his testimony for the bank when it's being sued by two parents for contributory negligence in the death of their son. Up to that point, Stephen had worshipped Jim for his genius. In the car on the way back from court, Stephen excoriates Jim, telling him that for all his own considerable intelligence and academic achievements, he could never do a thing like that. At the end of the film, we find out that Jim has been working against the bank all along. When Jim does essentially the opposite of what he did before - activate his program that he claimed can predict the stock marker, but is actually designed to bankrupt the bank - Stephen has another brief What the Hell, Hero? moment before desperately trying to reverse the damage.
After Rachel is poisoned by Crane's toxin, Batman loads her into the Tumbler, and then quickly rushes her back to Wayne Manor where he can administer an antidote, leading the police on a very spectacular chase, in which numerous police cars are destroyed - multiple ones taken out with caltrops, a few taken out by running into barriers, and few being crushed by the Tumbler. After Bruce sedates her in the Batcave, he takes the secret elevator up to Wayne Manor, where Alfred immediately delivers him this as Bruce is changing so he can look formal for his birthday party:
Alfred Pennyworth: When you told me your grand plan for saving Gotham, the only thing that stopped me from calling the men in white coats was when you said that it wasn't about thrill-seeking. Bruce Wayne: It's not. Alfred Pennyworth: What would you call that? [points to a breaking news report showing a helicopter shot of the Tumbler being chased down the freeway by police cars] Bruce Wayne:Damn good television. Alfred Pennyworth: It's a miracle no one was killed. Bruce Wayne: Didn't have time to observe the rules of the road, Alfred.
Bruce got one earlier in the movie from Rachel, when he reveals that he had intended to kill his parents' murderer:
Rachel Dawes: [slaps Bruce] Your father would be ashamed.
Contagion: Everybody jumps on Cheever for alerting his wife to get out of Chicago before the quarantine goes into effect, even though if she was sick, she'd have infected a lot of others.
Joker: I wanted to see what you'd do, and you didn't disappoint. You let five people die. Then you let Dent take your place. Even to a guy like me, that's cold.
He does it to Commissioner Gordon as well, although subtly:
Gordon: What have you done with him (Harvey Dent)?
The Joker: Me? I was right here (Shakes handcuffs). Who did you leave him with? Hmm? Your people?
In the same way, during the Joker's "social experiment", the Scary Black Man calls The Leader of the prison ferry boat on not throwing away the detonator immediately:
""Give it to me, and I'll do what you should have done ten minutes ago."
Prior to this, Batman pulls this on Harvey Dent after Dent hijacks an ambulance where one of the Joker's thugs is awaiting to be taken to the hospital after being shot in the leg, ties him up in a chair, and threatens to shoot him if he refuses to talk. Dent's coin turns out to have two heads, but he still abducted and threatened at gunpoint a mentally ill man—and no matter whether or not you intend to shoot someone with it, no gun is 100% safe unless it's not loaded (Even then, are you sure it's not loaded?). Batman calls him out on this breach of ethics, saying that Gotham deserves better from its "White Knight", and asks him what would happen if it got out.
Later on, the Joker brainwashes Dent into becoming Two-Face.
Batman himself receives one of these from Lucius Fox concerning the sonar technology he secretly circumvents into a mass-spying device designed to catch the Joker.
While the hero part is debatable, Dent, as Two-Face, does this to Ramirez after she delivers Rachel to the Joker:
Harvey Dent: (interuppting Ramirez in her excuse) "You didn't know what they were going to do to me." You're the second cop to say that to me. What exactly did you think they were going to do?
Dirty Harry: Got called out on the tactics that he used to bring Scorpio in, including his full-on Jack Bauer style interrogation on the football field. Granted, Harry was absolutely furious after Scorpio revealed himself as a complete sociopath (who didn't feel like revealing the location of his hostage after all), but it still qualified as What the Hell, Hero? in the eyes of Harry's superiors.
Enemy at the Gates has Danilov delivering a brief one to Vassili for wavering dedication. (While this would seem minor in other circumstances, it merits a 'what the hell' for a sharpshooter during the siege at Stalingrad.)
Ever After: After Prince Henry denounces Danielle in front of the entire court for lying to him about her true identity - in spite of being hopelessly in love with her - he gets an incredible What the Hell, Hero? speech from none less than Leonardo da Vinci.
The Expert: In this B-rated movie, the main character, disappointed by the justice system, decides to break in a maximum security prison and kill a convicted felon. His partner calls him out on this when he decides to share and go through with it, but the hero immobilizes him quickly.
Friday the 13th Part VI: Jason Lives: Tommy Jarvis demands to know why the sheriff didn't incinerate Jason when they recovered his remains. The sheriff gives him this reply in a very curt manner toward Elias Voorhees:
Ghostbusters: Ray Stantz for accidentally summoning the Stay-Puft Marshmallow Man.
The Godfather Part II: Though not exactly a Hero, Michael Corleone is called out by Tom Hagen when he plans to assassinate Hyman Roth - despite the fact that Roth knows his plots have failed, he's run out of places to run to, is implied to be terminally ill, and killing him is an unnecessary risk to business.
The Great Muppet Caper: Fozzie delivers one to all the Muppets when they all try to back out of Kermit's plan to catch the thieves who framed Miss Piggy red-handed:
Fozzie: Shame on you! I thought we were in this thing together. I'm just as scared as you are, but this has to be done! We don't want the bad guys to win. We gotta do this...f-f-f-for justice! For freedom! For honesty!
Neil Patrick Harris attempts to avert this at the end of the first movie by approaching Harold and Kumar, apologising for his role in the previous night's events, and offering to pay for their breakfast. They then launch into this trope anyway, leaving him to irritably point out that he's aware of the dick move he pulled, hence the apology-and-offer-to-buy-their-breakfast.
Also $200 for Harold's car. He made some "love stains" in the back.
Prince Nuada tells Hellboy that the nature elemental is the last of its kind; should Hellboy kill it, the world will never see its like again. (Then again, the elemental is only in danger because Nuada used it as a weapon in a crowded city. What the hell, villain?)
In the first film, Tom Manning accuses Hellboy of causing several BPRD redshirt deaths with his poor field leadership, and hits Red's Berserk Button by calling him a monster.
A History of Violence: Tom Stahl and his son Jack call each other out on their violent acts after Jack curb stomps two bullies:
Played for Laughs with Henry and Indy. When the two first reunite, they are quickly caught by Nazis. To escape, Indy snatches a machine gun from one of the soldiers and guns them all down. Henry is left shocked by his son's actions.
Played straight near the end of the film, when Jones Sr. gets free in the Nazis' tank, then takes control of one of its cannons and blows up a pursuing Jeep full of Nazis. Brody is horrified at this, but Jones Sr. curtly replies that "this is war".
Also, an instance of "What The Hell, Anti-Villain?" when Indy confronts Elsa in Berlin:
Elsa: You came back for the book? Why? Indy: My father didn't want it incinerated. Elsa: Is that what you think? I believe in the Grail, not the swastika. Indy: And yet you stood up to be counted with the enemy of everything the Grail stands for. Who gives a DAMN what you think?! Elsa: You do!
Iron Man 1: A variation, as Tony calls Pepper out for walking out now that he wants to protect everyone he's put in danger, whereas before she had no problem with his reaping the benefits of destruction.
Iron Man 2: Rhodey loses all his patience with Tony after Tony parties while wearing his Iron Man armor and using the suit's weaponry to amuse the guests. He decides Tony doesn't deserve the suit and hijacks the Mk.II suit to prove his point. Depending on how you look at it, there's Stern and all the people who aren't happy that Tony isn't sharing the Iron Man tech with the military.
James Bond in the reboot often catches a lot of flak from M and MI6 for using his License to Kill a little too liberally. In Casino Royale, he is nearly suspended for the unnecessary killing of a terrorist in a foreign embassy (or more accurately, being caught on tape doing it). In Quantum of Solace, M nearly arrests Bond when his reckless actions results in the death of Mathis and another MI6 agent, Agent Fields.
Vesper Lynd also asks Bond at one point if he was ever disturbed by the fact he'd had to kill a number of people to complete his mission. Earlier, Bond comforts her when she is greatly disturbed following the brutal killing of a warlord and his minions by Bond.
In Dr. No, Honey all but says the trope name after witnessing Bond (again somewhat unnecessarily) knifing a guard. This moment actually stands as the only time in the original film series (and the last until the Vesper moment described above) that someone is shown being upset at witnessing Bond using his license to kill.
Jaws: Mrs. Kintner, whose son was killed earlier in the film, proceeds to slap Brody in the face and call him out for already knowing that there was a shark roaming the waters prior to the attack. Brody, who feels he should done more to try and convince the mayor to keep the beaches closed, doesn't even try to defend himself.
Kamen Rider Fourze & OOO: Movie War Megamax: Kengo gets one from the Kamen Rider Club when he willingly calls up Foundation X to give away the SOLU that had taken the form of Nadeshiko Misaki...whom Gentarou had fallen in love with.
Kicking & Screaming: In this 2005 Will Ferrell movie, Phil Weston (played by Ferrell) starts employing draconian measures in the training of his Little League soccer team in order to get them into the finals, including sending his own son Sam onto the bench and preventing him from contributing (an act his own father pulled on him in his childhood). Weston's wife Barbara finally gets fed up and calls him out on his newly-acquired Jerk Ass behavior:
Phil: (Sam) can play if he wants to...
Barbara: He'd love to play for you! But every time he tries, you end up putting him on the bench. (gives Phil a look) Sound familiar?
Phil: But I just wanted to get us into the finals.
Barbara: Well, congratulations. You made it. (walks away in disgust)
Happens in Maleficent when the titular character's servant, Diaval, calls her out on giving up on breaking Aurora's curse, even though he knows she cares about her.
Mean Girls 2: When Abby finds out that Jo accepted money to be her friend, she takes it about as well as one would expect.
Greg thinks Jack is still in the CIA and is planning an operation. He plays that card when the entire Burns family has turned against him, hoping to make Jack the bad guy. It turns out it was a honeymoon for Pam's sister and her husband.
Jack gets a taste of this himself a few scenes later from Pam and his own wife over his unreasonably over-protective and over-controlling nature and refusal to cut Greg any slack whatsoever, as evidenced by the fact that, having learnt that his efforts to prove that Greg couldn't have been a doctor if he wanted to were wrong because he wasn't looking under Greg's real name, Jack immediately — and hypocritically, given how much sheer effort he went to to prove Greg wrong — comes up with another reason to not like Greg, proving that he's just determined not to give him any quarter at this point:
Jack: Oh, honey, what does it matter? Look at this place! He almost ruined the wedding because he lied! Pam: I love you, Dad, but you can be a real jerk sometimes. [storms off] Jack:[Taken aback] So what if he took the MCATs? He's still not good enough for Pam. Dina:[Fed up] Who is, Jack? Nobody has ever been good enough for your Pam. I mean, do you realize that you never even warmed up to Kevin until she broke up with him? Maybe it's time you think about what Pam wants.
And then a few scenes after that, Greg gets the opportunity to put Jack in his place as well.
Mystery Team: Jason is given this treatment on several occasions by his friends.
Necessary Roughness: After the hapless Armadillos managed a tie against Kansas, a group of boosters reward the team with sportsjackets as a token of appreciation and a sign of "Keep it up and this is only the start." Coach Generro stumbles onto the proceedings, then forces the team to line up and give the gifts back on the spot (Generro had bad experiences with boosters in his previous job). When the team has left, Coach Riggendorf lets Generro have it for turning what should've been a moment of awesome (it was the team's first taste of any sort of success) into a Humiliation Conga.
Orgazmo: The whole plot involves Elder Joe Young, the protagonist and a Mormon missionary, getting involved with porn acting to make enough money to pay for a temple wedding for himself and his painfully wholesome fiancee, Lisa, as well as get them a nice place when they're married. Lisa herself unfortunately finds out about his acting in pornos when she decides to pay him a surprise visit. She is not happy about it and tells him so.
The Other Guys: A reporter asks Highsmith and Danson if it was worth the remarkable amount of property damage to capture a few men who, after a spectacular car chase, turned out to only have committed the crime of possession of a very small amount of marijuana.
The Purge: James Sandin doesn't hesitate to yell at his kid for letting a stranger into their house, because they don't even know who's after him. It turns out that he has a point when the psychopathic gang turns up on their doorstep....
Revolution 1985: Daisy accuses Tom of cowardice for quitting the Continental Army when the British drove them out of New York City. Tom retorts that the entire army fled.
It is notable that Zoe didn't actually disagree with anything Mal said or did, and offered no alternative solutions. It seemed like the incident just left her with a bad taste in her mouth and she wanted to see if it did for Mal too.
Spider-Man 3: Eddie Brock calls Spidey when Spidey destroys his camera.
Starsky & Hutch: Starsky gets called out for chasing a purse-snatcher halfway across town, through rooftops, and landing on the roof of a car.
Lily confronts Picard over his fight with the Borg, asking how many people had to die for him to save the ship? She invoked Moby-Dick, comparing him to Captain Ahab...though when he did finally come to his senses, she admitted she never actually read the entire book.
There's also the scene where he gets called out after killing a Borg revealed to have been a crewmember, and he tries to claim there was no other way to save him... this from a guy who used to be called Locutus of the Borg.
It was an entirely different case though. Locutus was purposely left partly human and individual to serve as emissary of Borg and as sidekick to the lonely and also individual Queen. And it took lot of medical expertise and time to "deborg" him. Although even standard drones can be liberated, facing the facts that they are stranded in the past and the ship is being overrun by the Borg, it was a good call. The chances of assimilated crew members being retrieved were MUCH thinner than the chance they would end up in eternal slavery.
Star Trek Into Darkness: Kirk gets called out by Pike for falsifying his report regarding his mission to Nibiru in the opening.
Kirk gets a big one when McCoy calls him out-forcefully-for forgetting the fact that it's been two-some years since he commanded a starship, and that his unfamiliarity with the Enterprise's refitted systems is putting the whole ship in jeopardy. Surprisingly, Kirk actually listens. Apparently, even the greatest captain in Starfleet history isn't immune to hubris.
Of course Kirk didn't relinquish command and instead assigned Decker, the rightful captain of the ship, to an advisory role. Decker remains rather bitter about it throughout the rest of the film.
Kirk blazes with Ahabesque fury, "Let them die!" when told by Spock the Klingons will be extinct in 50 years; Spock's reaction is one of such grave incredulity that it even forces Kirk to collect himself and change the subject. William Shatner was disturbed by Kirk's Face-Heel Turn, and had Meyer shoot the scene again with Kirk being more reasonable. Meyer went to the original take in the final cut. Spock gets his own "What the hell" when he mind rapes Valeris. Of course, Kirk getting called out for hating the Klingons makes him look even worse when you consider that, back in The Original Series, he called out an Enterprise lieutenant for expressing very similar opinions toward the Romulans. Hell, both of them were motivated by loss of family (the lieutenant lost several family members in the Earth-Romulan War).
Spock gets this from Kirk and most of the crew when he "volunteers" them to meet for the first peace talks with the Klingons. This seems exceptionally stupid considering the Klingons had earlier accused Kirk of developing the Genesis device as a superweapon and had killed his son. The conspirators have no problem leveraging Kirk's reputation to derail the peace process.
Kirk gets this again later from McCoy after Marta helps them escape from a Klingon prison and once free, he decks her. After hearing McCoy thought he had gone crazy, he theorized that their escape was too easy and that Marta had betrayed them.
Young Magneto goes into an outburst about how fellow mutants were being killed left and right while Young Charles has been in hiding with Hank.
Erik: Angel, Azazel, Emma, Banshee. Mutant brothers and sisters, all dead! Countless others, experimented on! Butchered! Where were you, Charles?! We were supposed to protect them! Where were you when your own people needed you?! Hiding! You and Hank! Pretending to be something you're not! You abandoned us all!
Before that, Logan calls Charles a little shit for his cavalier attitude about the future.