In The Dead Past, the government agents trying to prevent the protagonists from learning the secret of viewing the past seem like a classic heavy-handed Government Conspiracy... until it turns out that they're simply trying to prevent privacy from being utterly destroyed by the dissemination of devices that can view any place at any past time from a century ago to a microsecond ago.
"Happy goldfish bowl to you, to me, to everyone, and may each of you fry in hell forever. Arrest rescinded."
The short story In A Good Cause... follows two friends over decades as their paths diverge, one of them an idealist desperately trying to unite the human race in the face of an alien threat, the other a soldier and later a political leader who fights in multiple wars against other human factions. When the aliens finally do attack, the human factions unite and make short work of them. The soldier points out to his friend that decades of internal competition had forced humanity to advance militarily, which protected them from outside invaders. Though events have proved him right, he acknowledges that his friend's idealism will make him a hero in the future, while his own militarism will make him history's Designated Villain.
Georgie, in A Clockwork Orange, is a vicious, amoral hoodlum. That does not mean that his proposal for the gang to start concentrating on crimes that bring in worthwhile profit is wrong. Under Alex's leadership, they're running the same risks for meager, if any, reward.
And when Alex screams that "Beethoven did no one any harm! HE JUST WROTE MUSIC!" he, too, is quite correct.
John Farson, the "Good Man" of The Dark Tower, is a cruel, power-hungry despot, or so we're told. However, he's right that the Affiliation is ruled by a cabal of thugs with vague aristocratic pretensions who maintain power largely by having the best guns.
In the first Disney Chills book, while Ursula is a nasty villain you don't want to be making deals with, she rightly chastises Shelly for using the ocean as a dumping ground for trash, and Shelly reflects that she knew throwing a coffee cup in the ocean was bad but did it anyway.
In Firestarter, the Shop's methods are reckless and dangerous, but they cannot be faulted for wanting to get Charlie and Andy under control. Either of those two, alone, is hideously dangerous, and the two of them together could cause untold havoc.
The Shop is also unfortunately correct in wanting to keep the two in custody, reasoning that if Charlie's abilities were to become widely known, virtually every other power on earth would stop at nothing to gain control over her. As misguided as the Shop is for planning to use Charlie's abilities for its own ends, in its own twisted way it's keeping America safe.
Another King villain (or Anti-Villain, depending on the interpretation) is Jack Torrance. While he's chasing Danny, he notes that Danny took the master key and went into Room 217, despite being expressly forbidden to enter any of the guest rooms. Danny had also promised Hallorann he wouldn't go in there, so some of his problems might have been avoided if he'd behaved.
Vito Corleone is, for all his Affably Evil ways, a ruthless, murderous gangster. Which does not make his statement that he and his colleagues are morally superior to "the pezzonovanti who have killed untold millions in our own lifetimes" to his fellow Dons one whit less correct.
In Gone Girl, Amy brutally deconstructs the Manic Pixie Dream Girl trope by bitterly monologuing about the inherent unfairness of women being expected by society to change their personalities to suit male needs and get labelled as shrill, nagging bitches the minute they have differing opinions or interests to their partner. Though she is pretty hypocritical because she ultimately forces Nick into being the ideal man she wants him to be by threatening to turn the American public and his unborn child against him, she's not wrong in pointing out the massive Double Standard.
Grimoire’s Soul: Towcard may be willing to kill Medhi because he's learned too much, but he's also quite correct that Kesterline's social system is built on nothing but lies, even if he breaks it to Medhi in the least kind way.
The Hobbit: While Bilbo speaks with Smaug, the wicked and greedy dragon brings to the hobbit's attention something he hasn't thought about concerning the Company's quest to take Erebor back from Smaug; even if it were possible for the hobbit to claim his promised share of the treasure without Smaug having a say in it, he couldn't get far away with it all. Despite knowing that Smaug is trying to play mind games with him, Bilbo cannot help but be troubled to realize this.
Annie Wilkes in Misery is very perceptive in her criticisms of Paul's writing, and Paul concedes this. He especially agrees with her scathing dismissal of Cliffhanger Copouts and Deus ex Machina, and eventually comes around to her dismissing Fast Cars as pretentious. After all, it is not her criticism that's bad its how seriously she takes it.
In Percy Jackson and the Olympians and its sequel series, the main villains want to overthrow the Olympians and take over the world in their place. Should they succeed, it would lead to the total collapse of civilization and the enslavement, if not outright destruction, of humanity. That being said, many times they bring up the valid point that the Olympians themselves can be unbelievably petty and cruel, even to those that don't deserve it, and that they can often be inattentive or uncaring to the mortals that need and look up to them. One of the major reasons the bad guys in the first series had an army of demigods on their side in the first place was due to their feelings of abandonment, believing themselves to be forsaken not just by the gods, but by their own parents. Even the main characters admit at several times, that while the Olympians may be overall better than the villains they are fighting against, they sure as hell aren't what they would call good.
In the Rivers of London book Lies Sleeping, Lesley tells Peter that the City of London itself is a kind of vampire; that it sucks in jobs, talent, money, and people from the rest of the UK and gives nothing back, and that to most people in the UK the entire of London could drop into a huge hole in the ground and they wouldn't give a damn about it. She might be The Dragon to a megalomaniacal bad guy who plans on conquering the UK to bring in a new Dark Age, but she's not exactly wrong. Many of Peter's own monologues have been about how firms, people, and transport links all end up in London.
Eöl the "Dark Elf" in The Silmarillion is a selfish, secretive Domestic Abuser who eventually kills his wife while trying to kill their son.. But he does have a legitimate reason for hating his wife's Noldor kinsman (apart from the fact that he is a controlling jerk). Many of the Noldor are themselves villainous, arrogant, xenophobic, domineering, and they killed many of Eöl's relatives in the First Kinslaying. Shunning the Noldor at large in favor of dwarves and other elven people is not unreasonable, although the rest of his behavior is inexcusable.
In Simon Bloom, Sirabetta, the Big Bad of the first book, is quite correct on how the Knowledge Union has some significant flaws.
In Charlaine Harris' ''Southern Vampire'' stories the anti-vampire forces insist that vampirism is not, as claimed by the newly-out vampires, a medical condition, not all vampires will be completely content drinking synthetic blood, and that vampires have a secret government whose laws they consider more significant than human laws, if only because its punishments are more sure and more brutal... and they're right. (They may get the scale wrong, e.g. most vampires adjust to synthetic blood pretty well and stick to willing human donors if only to avoid trouble.)
In Those Who Hunt the Night, Grippen, the Master Vampire of London, may be a remorseless killer of thousands over his centuries-long lifespan...but he's perfectly correct to point out that the governments waging World War I have slaughtered far more in a month's time than all the vampires of Europe could do. He also points out that he and the hero aren't so different, referring to the hero's past as a secret agent who did his share of killing.
Victor Dashkov from Vampire Academy is portrayed as a villain, but sees himself as a social reformer. At several moments in the story Rose finds herself agreeing with some of the things Victor advocated, including a reorganisation of the Moroi government.
Victoria is unusual for placing an intelligent Nazi true believer in this role. Captain Halsing's ideology is, of course, itself described as rather unsympathetic, but he nonetheless makes valid points when he exposes the inconsistencies and flaws in the heroes' own right wing libertarian-ish beliefs.
She may be slightly biased given that her trigger event was caused by the sadism of a young hero, although really this just supports her argument.
The Scarlet Pimpernel: While the author, the Baroness de Orczy, clearly has little sympathy for the government of the First Republic and pretty much outright calls the Reign of Terror a genocide, she admits that the pre-Revolution government was arbitrary and cruel to commoners to the point where revolution was in fact justified. Several moderate republicans are treated sympathetically, as are people who fought back against abuse by noble rulers.
When defending their actions against Nie Mingjue, they bring up a good point how one's standing in life determines how valid others find their actions and words to be. Those with money and/or authority are able to get away with their actions and words compared to those who don't have such privileges.
They aren't wrong when they tell Lan Xichen that no matter what they achieves, regardless of the means they would employ, it would all be ignored and disregarded simply because their mother was a prostitute.
In the climax, they tell Wei Wuxian that no matter what action he takes and no matter the efforts Wei Wuxian takes to defend the people, the rest of the cultivation clans would always see him as an enemy and The Scapegoat.
They also call out Jiang Cheng for allowing his pride, envy and insecurities regarding Wei Wuxian to strain his relationship with his martial brother whereas Wei Wuxian would have been protected from the other clans if Jiang Cheng simply trusted Wei Wuxian more.
