Witch Hunter Robin does this a lot in the second season. Every witch encountered by Robin thus far has gone power mad and evil...but then she begins encountering witches who engage in moral shades of gray and, finally, witches who are guilty of nothing but being picked out by her organization. And they're the humane ones; it's implied organizations outside of Japan kill witches flat-out and the only reason her organization keeps witches around is to produce the magic suppressor "Orbo" from their bodies. In one episode, it's implied that the organization systematically destroyed the career, marriage, and finances of a potential witch who had never even used his powers. Destitute, he's forced to use his power to defend himself from some thugs and is taken in, put through some kind of magic lie-detector, and given the choice to admit he is evil and join them or die for using his powers.
Inu Yasha plays on this occasionally; all humans fear youkai and hanyo, but not all youkai and hanyo want to hurt humans. One example is the "Spider-Head" arc, where the girl Nazuna exhibits considerable prejudice towards Inuyasha and Shippo, despite Inuyasha having saved her from a fall. The Gentle Giant hanyo in a side story also counts. He's generally too gentle to hurt anyone intentionally (unless they're hurting his human mother). In another episode, they meet a morally gray demon hunter who condemns Rin and Kagome for even associating with demons/youkai and half-demons/hanyou. This trope is even inverted with a villain who is convinced that all humans want to hurt demons.
In Hellsing, the Catholic-founded Iscariot Organisation sees vampires as an abomination and affront to God that needs to be wiped out, even the vampires that are hunting other vampires for the sake of humanity. It loses its edge, however, when you consider that, until Seras came along, there was only one such vampire, and he's a sociopathic slaughter machine that is only held back by a very mortal woman.
The demon hunters in Omamori Himari seemingly want to eradicate all demons, with minor exceptions (currently only one) like the Amakawa family, who have some demons as servants.
In contrast with Hellsing, in Chibi Vampire, vampires usually only take enough blood to make the person feel anemic and drained of emotion (which can actually be a good thing, if a person has a lot of negative emotions). So it's not surprising that Vampire Hunters are portrayed as Knights Templar.
Witches suffer from this in both directions, because many monsters are prejudiced against them for being "almost human".
Bleach has Ichigo and co. acting like this when they meet Nell Tu and the others. Ichigo comes very close to killing the Hollows, which is understandable, due to the Hollows chasing Nell as a game of tag. Once the misunderstanding is cleared up, they join forces, despite the previously-held belief that Hollows were Always Chaotic Evil. Apparently, the Hollows are just mostly chaotic evil.
Izuna, the amateur exorcist, also had a bit of this going when she first met the Sorcerer Kitsune Tamamo and the Snow Maiden Yukime. But these two are far beyond her level and handily humiliated her before Nube set her straight. Unlike Yang Kailen, though, Izuna is a lot more open minded (she keeps and breeds her own Tube Foxes) and gets over herself.
Nube's father is also guilty of this, to the point of attacking Yukime on sight merely because she's a youkai and he's an exorcist.
Once it's clear demons are infiltrating human society in Devilman, humans start military actions against them. The problem is that they don't know and later don't believe in Devilmen - humans who bonded with demons and retained their good nature - killing them alongside real demons. They're also willing to kill anyone even suspected of being a demon and those accused of helping them.
The comic book series Wolff and Byrd has a restraining order served to a woman whose "sacred duty" is to hunt down and kill vampires, in what's obviously a take on Buffy.
Captain Britain and MI-13 recently had an arc where Blade (yeah, that one) joins the team to deal with a supernatural menace. Spitfire, who shows vampiric traits due to a WWII-era attack by a vampire, is on the team. When Blade first meets her, he tries to stake her. They soon end up in an Enemy Mine situation (Dracula launching vampire missiles at Britain from his castle on the moon). They later start dating, making the attempted staking an unorthodox Meet Cute.
After being paralyzed by Shockwave when the Decepticons attacked an advanced oil rig she was working on in the Transformers comics, Josie Beller developed an advanced suit that allowed her to walk as well, as granting her superpowers. As Circuit Breaker, she vowed to take the fight to the heartless machines that had crippled her. The problem was, she neither knew nor cared that there were two factions of robots, and that one of them was trying to help the humans. Her hatred did not distinguish between Autobot and Decepticon, and she often wound up doing more harm than good, especially as the Autobots refused to harm her.
The Termight Empire in Nemesis the Warlock is built on committing these. There are genuinely malevolent aliens out there, but they are very much in the minority and in no way justify the Empire's policies.
Films — Animated
The core Aesop of Disney's Beauty and the Beast is about vanity and selfishness, and not getting obsessed with appearances. Gaston riled up the crowd to this trope, but he himself is not guilty of it. He wants to kill the Beast because he sees him as competition for Belle. He also has no trouble believing the Beast is harmless, but, being a Jerk Ass, he actually mocks him for it.
Films — Live-Action
The vampire movie Blood Ties (no, not based on the Canadian series) takes this trope to a whole new level, with a group of vampire hunters who appear on a Jerry Springer knock-off and sound a lot like the Klan.
Averted in Van Helsing (ironically enough), where Van Helsing is reluctant to kill Frankenstein's monster because he can see he's not actually evil, and Van Helsing does seem to feel remorse for having to kill people who've become monsters, like werewolves and Dr. Jekyll.
I Am Legend was intended to lead up to this, and still does in the alternate ending on the DVD release.
In Lucio Fulci's Don't Torture a Duckling, the townspeople blame a string of child murders on a reclusive, unpopular, Hollywood Homely witch and lynch her based on zero evidence. The murders continue.
Fido depicts an alternate reality where zombies have been domesticated by collars that suppress their urge to feed. However, Bill Robinson hates them even though the titular zombie is shown to be capable of compassion even when his collar malfunctions.
The Dracula Tape by Fred Saberhagen, where Dracula is a mostly harmless individual who's harassed by the Harkers (who are clueless) and Van Helsing (who's a religious fanatic). Which means that is a case of a Van Helsing Hate Crime committed by... Van Helsing.
Dealt with extensively in one section of Night Watch. Forces of darkness and light exist, but have a treaty keeping each other in strict balance. Enter a guy who only knows that he can sense evil and it must be eliminated. It doesn't help that he's part of the darkLight side, and in this universe, you can't switch sides.
The issue... comes up, shall we say, in Liz Williams Snake Agent (her first Detective Inspector Chen novel).
A major plot point in the Kitty Norville series. It takes place in The Unmasqued World, and a lot of people aren't happy to know that werewolves and vampires (and a lot of other things) are out there. At least four of the novels so far have featured normal humans treating Kitty like she's a monster, from accusing her of mauling cows with no evidence of it to trying to kill her.
Not to mention that the whole reason the Masquerade was broken was due to a hunter attacking her on air.
The titular Night Huntress is convinced that all vampires are bloodsucking demons. After she learns that not all of them are evil, she realizes that some of the vampires she killed may just have been looking for a snack and a one night stand, and killing them may not have been self-defense.
The Palatine Guard of Meg Cabot's Insatiable series see nothing wrong with torturing a captive vampire, especially since nothing short of outright killing one would leave any evidence. Alaric Wulf, one such Guard, repeatedly makes the argument that since the Big Bad who gravely injured his partner is a vampire, he is fully justified in summarily killing any and all vampires he meets, and any human who dares harbor one. In the first book, during the climactic battle against the Big Bad and his minions, the Palatine Guard repeatedly shoot the vampire protagonist Lucien in the back (he survives because he is just that Bad Ass). For some reason that will presumably be explained in the next book, all this inspires the female protagonist Meena to join the Palatine Guard.
Happens in P N Elrod's book Quincy Morris, Vampire, which follows the story of the man who killed Dracula when he rose as a vampire himself. Trying to convince Van Helsing that he only drank animal blood wasn't very effective. In story, his type of vampire is compared to a hunting dog vs Dracula's vicious wolf.
I Am Legend is the Trope Codifier, if not the Ur Example. Robert Neville, the last human on Earth, spends his nights being tormented by vampires trying to get into his house and his days finding and slaying the creatures in their sleep. The title of the book comes from the end, where Neville discovers that some of the vampires have learned to stop acting like monsters and have begun to form a new society. Since Neville was unaware of their presence, and he's been slaughtering vampires indiscriminately for years, he's slain a large number of the good vampires. Neville realizes to his horror that they view him as a monster, and he takes a suicide pill before they can execute him.
This is raised by Peter in Moon Over Soho along with the thorny problem of Inhumanable Alien Rights when it comes to sapient individuals who are carrying out paranormal crime. He makes the point that the courts are the place to deal with them, not just arbitrarily hunting them down and executing them. Ultimately, the author chooses to Take a Third Option in resolving it.
In the Lonely Werewolf Girl books, the guild of Werewolf Hunters has no backstory to explain exactly why they are hunting werewolves, so tends to come across as this. Especially since their targets include a fashion designer, a pair of tourists, a pair of punk singers, and their manager.
Tanya Huff's Blood Trail centers around this. The protagonist is called in to discover who's been murdering the local pack of werewolves; it turns out to be a religious neighbor who'd discovered their nature and decided to do God's work by killing the soulless abominations. When one of them saves his life, he realizes how badly he was mistaken and, unable to deal with it, kills himself.
Discussed in the Discworld Watchmen books, most recently with goblins in Snuff.
The Dresden Files loves to play with this trope, given that it's a fantasy series and also a detective serial, so they are obligated to use every "things are not always as they seem" in the book:
Played Straight: Harry's interactions with the vampires can initially and later literally be called "genocidal", but later in the series, it's made clear that they are not necessarily evil or even harmful, with several vampires of various types joining his list of regular contacts.
It's worth mentioning that there are several types of vampires in the Dresdenverse: the Black Court are unholy abominations against life itself, the Red Court are demons in human suits, and the White Court are Emotion Eaters. Most of his contacts are in the White Court, since they're much more human than the other types of vampires.
It is more that the White Court prefer to rule through subterfuge and manipulation. The Black Court want to kill and slaughter and the Red Court want to subjugate through force (and are at war with the Council). So the White Court are definitely still, by and large, evil and dangerous. But in a manner that is a "lesser of two evils" kind of way.
Averted: The Knights of the Cross, called by God to hunt evil and defend the innocent, are actually quite reasonable, understanding people who take the stance that redemption is within anyone's reach, human or monster. Eventually, they reveal that their core purpose is to redeem people possessed by literal fallen angels, up to that point presented as their worst enemies.
Subverted: Suspecting a supernatural creature of a crime due to Fantastic Racism, then finding out that said creature was actually the Red Herring and a decent guy to boot is one of, if not the primary plot device of the series.
Highlander had James Horton and the Renegade Watchers from season 2 who wanted to kill all of the Immortals, believing them to be perversions of nature. This is turned around in the two-part episode Judgment Day/One Minute To Midnight. Immortal Jacob Galati is killing off all the Watchers (good or bad), after Horton and his followers killed his wife, Irene, and tried to do the same to him. He didn't care that most of them were innocent.
Buffy the Vampire Slayer mostly ignores this in the earlier seasons, until it is tackled head-on with the Initiative in season 4. They lump every non-human under 'evil', even going as far as experimenting on an untransformed, conscious werewolf. In the episode "Phases" Buffy goes up against a werewolf hunter who sees nothing wrong with the fact that a werewolf is human 28 days of the month, but he is more of an amoral, greedy monster hunter than a bigoted, fanatical monster hunter. Out of universe, there were plenty of online forum debates about whether Buffy was right to kill vampires when one (Spike) displayed the capacity for redemption; if one can, they all can, and therefore Buffy is wrong to deny them that opportunity, ran the argument.
Angel, on the other hand, dealt with this trope head-on, when it turned out that Gunn's old demon-slaying gang had started turning its sights on all demons, no matter how harmless they were.
As the series progressed, Angel became like a Gothic version of Star Trek in a lot of ways, in the sense that demon was a catchment word which described a lot of different species; and though plenty of them were evil, in some cases, the word demon didn't rightfully imply anything negative about them at all. In the case of characters like Lorne and (later) Illyria, the value-neutral term extraterrestrial would have been a lot more appropriate.
Holtz, who — well, suffice it to say, Angel's vampirism is only Holtz's second most pressing reason for wanting him dead. Holtz is fully aware of Angel's curse, but unlike most other characters, he denies that this makes any ethical difference: "I will never agree that he has somehow been absolved from the past by the presence of his soul." Given his historical timeframe, this is pretty accurate for Holtz. Angel and Angelus are, essentially, the same being to him. That Angel feels bad is fine and good, but it's really up to God to forgive him if God feels Angel's suffered enough. Until then, Angelus has escaped mortal judgment time and again and is still an abomination.
Holtz's attitude is actually very similar to Angel's own - both consider Angel responsible for what he did as Angelus. It's just that Angel is trying to make up for it while Holtz thinks he needs to die. Angel can never really make the claim that Holtz is wrong for pursuing his vendetta. He doesn't even try.
The first season episode when a gang of demons arrive in LA and start killing 'abominations'. That is, any demon who is even slightly human or half human, like one of the main characters, Doyle, or any vampire at all. According to the previous Buffy finale, they weren't purebloods themselves, either. The Nazi analogy isn't all that subtle, is it? This is the Angel theme. Some monsters aren't so bad!
Goes on the assumption that all monsters are naturally evil, but occasionally throws a curve ball, like when Sam and Dean encounter a group of vampires who abstain from human blood and feed on cattle. Gordon Walker, however, sees no difference between them and any other vampire, and Sam and Dean have to stop him from killing them all. However, later seasons have stressed the moral issues of the job of hunting, as it has been revealed that most of the major threats, including demons, were human at some point
Also contains an example in Sam, who is eventually revealed to have psychic powers and demon blood in him. Although Sam is a hunter with good intentions throughout (even if those good intentions don't always bring good results), Gordon is dead set on killing him because he makes no distinction between good and evil when it comes to the supernatural and cannot be convinced that Sam is on their side. This eventually leads to Gordon's death. By barbed-wire decapitation.
Benny, a vampire Dean met in Purgatory who helped him escape on the condition that he took him with him. He claims to be surviving off of stolen blood transfusions and so far there hasn't been any evidence he's lying about this, but that hasn't stopped Sam from wanting to chop off his head since the moment they met.
The Hunters on Teen Wolf seem to go this route more often then not. Although in theory they have a Code that restricts them to hunting only werewolves that harm humans, most of them seem to have little problem with ignoring it and killing any werewolves they find. They have actually developed such a self-righteous attitude towards their mission that they are even willing to torture and kill ordinary humans if it suits their goals, whether those humans actually have anything to do with werewolves or not. Combined with how well-equipped they are and the way that they generally outgun their victims by a wide margin, this creates the impression that they are thrill-killers rather than protectors of humanity.
Their willingness to tolerate Scott is due to a complicated mix of him being a minor, not having killed anyone and being important to Allison. Even so, this is a very tenuous tolerance as shown by Gerard stabbing Scott in the gut and Victoria trying to murder him because they were still dating despite their having been ordered to break up.
On Big Wolf on Campus, "Muffy the Werewolf Slayer" showed up, intending to hunt down and kill the protagonist; she was eventually convinced that, no, honest, Angel Tommy was a goodvampire werewolf, though she found the concept pretty freaky. (Every other werewolf seen on the show is at minimum a Punch Clock Villain and more likely a man-eating psychopath, so her surprise is understandable.)
In a unique variant, Friday The 13th: The Series once featured a hunter who killed humans in order to empower a cursed cross he could wield against vampires. Granted, the vampires in question weren't necessarily of the Friendly Neighborhood variety, but this guy's priorities were clearly whacked.
True Blood is a HBO series based upon the Sookie Stackhouse novels by Charlaine Harris. Harris' vampires have "come out of the coffin" politically speaking, and since, naturally, "God hates Fangs," there are more than a few religious types who find this disturbing.
The UK miniseries Ultraviolet centers around the moral progression of the main character after he kills his friend-turned-vampire and joins up with the people hunting them. According to them, vampires, or Code Fives, are a "public health problem" who must be neutralized before they can organize any further. When it's revealed that the Code Fives don't actually murder their prey, but, even more importantly, are close to designing viable synthetic blood, Michael's role begins to change.
A Grimm inevitably has this reputation among the creatures hiding their presence by living among humans. As Grimms have the ability to see them for what they really are if they lose control, they've historically been known to mercilessly hunt and slaughter non-humans. Nick, however, being a police officer, tries to treat them as he would anyone else once he figures out what's going on, and prefers to arrest the ones who break the law whenever possible, rather than hunting them. That said, even the ones who legitimately try to live normal lives can be extremely dangerous. Even Monroe, the Friendly NeighborhoodBig Bad Wolf, only says that he doesn't kill people anymore and ended up ripping a guy's arm off when he lost control in a fight.
Father Kemp of Being Human has no qualms in killing most of Bristol's vampire population, kills werewolves under the guise of helping them, and forcibly exorcises ghosts. He does this in spite of a good number of them actually being decent people just trying to live a normal life.
Vampire Diaries plays with this a great deal - on a few occasions, ruthless vampires framed more peaceful ones for their crimes and let the town's indiscriminating Council kill them. Of particular notice is Bill Forbes, who attempted to torture his daughter in an attempt to teach her not to be a vampire. More recently, the repeated deaths of Alaric Saltzman allowed the ancient witch Esther to turn him into one of these, to the extent that he brutally murdered other Council members for their failure to kill every vampire.
Used towards the end of Season 1 with the Founders Council and in particular with 'Uncle John's' arrival in town - mainly as he was such an unsympathetic jerkass. May be a Broken Aesop as some, if not most, of the vampires really are amoral killers that need to be put down, and even the 'good' ones can go off the rails on occasions. Compare with other vampire shows where this trope is taken even further.
Mind you, part of the problem with Uncle John is that he seems prepared to team up with some of the nastiest vampires out there to kill off friendlier ones... and is prepared to risk humans for a chance to kill vampires.
Emil Danko of Heroes has the job of capturing evil people with powers. However, he hates everyone with an ability and rounds them all up.
This happens - sorta kinda - in Clarimonde, 1998 TV adaptation of La morte amoureuse by Theophile Gautier. The title character is an old witch who keeps herself alive and beautiful by having sex with the Catholic priests. She does not rape or hurt the men, but in the end she is killed.
In Reckoning, viewpoints range from "Kill 'em all" (Avenger) to "Kill 'em when they threaten humanity" (Defender) to "Study them, and use that to your advantage" (Visionary) to "Some of them can be cured" (Redeemer) to "They can be good people, too" (Innocent).
In Vigil, the Compacts and Conspiracies range from new media visionaries who wish to study and expose the paranormal, to fundamentalist Christians who want to "redeem" monsters, to Church Militants who view monsters as demons, to debauched aristocrats who kill monsters because it's fun.
Even outside of direct hunter-monster interactions, werewolves in Werewolf The Apocalypse are strongly encouraged by their elders to destroy anything associated with the Wyrm and are quite capable of dusting vampires, even though not all vampires in the setting are reliably evil; this antagonism does not appear in the spiritual sequel Werewolf: The Forsaken.
Likely to pop up in Exalted (another fine White Wolf product).
Most player characters, larger-than-life heroic badasses by default, are bound to have to deal with the fact that a great many people consider them demonic "Anathema" out only to tempt them into straying from the "one true faith" (the Immaculate Faith)... and that there are quite a few powerful individuals and factions around who'd just as soon see them safely dead once they learn of their existence. All this while trying to save the world from all sorts of genuine threats...
This can also happen to Abyssal and Infernal Exalted, which are usually the evil champions of said genuine threats. Not all of them are bad, however — it's possible to play either type as a hero or anti-hero. But other Exalted, even outside the Immaculate catechism, may well decide to fight them as part of the general struggle against the Deathlords, Neverborn, and Yozi. It doesn't help that Abyssals are largely Walking Wastelands whether they like it or not, and the Infernal Green Sun Princes are all slowly turning into Eldritch Abominations.
Rudolph van Richten, Ravenloft's greatest monster-hunting expert, could have gone down this path, but chose not to let hatred rule his life. His books on ghosts, werebeasts, witches, and Vistani address the possibility that a "monster" may be inoffensive and/or unwilling; other Ravenloft monsters are so irredeemably evil and destructive that the hate crimes are justified in their case.
The Anvilicious Call Of Cthulhu adventure 'Gothic' from the modern day Goatswood campaign book, in which the scenario writer clearly states that the PCs are expected to sympathise with a couple of vampires who 'just happen to be' gay. Quite apart from issuing victim status to a pair of undead parasites, the scenario then goes on to indicate that all of their antagonists are raving bigots and to give us all a large dose of Christianity is Catholic in a way that doesn't sit too well with its rural English setting. Needless to say, this adventure takes a lot of re-writing to be playable.
Witch hunters in Witch Girls Adventures range from comparatively decent sorts who try to target witches that are actually a problem for people and are willing to let children off with a warning, to the Malleus Maleficarum, who take Van Helsing Hate Crimes into Knight Templar territory, being perfectly willing to kill (relatively) harmless witches and children, and whose ultimate goal is the complete genocide of witches.
Dungeons & Dragons. Despite supplements that directly oppose this, many gamers assume that Evil=Ok to kill, with or without another reason.
Some supplements that oppose the idea of killing evil do so by assigning the evil alignment (in terms of a statistics block) to characters who are in no way evil in thought or deed. So they don't really oppose the idea that evil = okay to kill so much as they dispense with any meaning behind the terms "good" and "evil" beyond how they affect spell mechanics.
In older versions of D&D, "Lawful" implied good and "Chaotic" implied evil. "Old School" D&D derivative Lamentations of the Flame Princess uses Lawful to mean "assigned a destiny by higher powers" and Chaotic to mean "aware of incomprehensibly powerful cosmic forces that could engulf our world any day now". There's no moral code or philosophy attached to either alignment; spells that detect "good" or "evil" merely detect entanglement with these powers/forces, although characters may not see it that way. Notably, all Clerics are Lawful and all Magic-Users (and Elves, who use MU spells) are Chaotic.
A slightly less common, but still all too regular occurrence, is for players to forget that there aren't actually all that many races that are all Evil. Killing evil without other provocation may be borderline, but killing someone without provocation because you wrongly assume that they are evil...
The Eberron setting comes flat out and says that there are no Always Chaotic Evil races (well, maybe the daelkyr). An orc or goblin is about as likely to be a respectable merchant as a bloodthirsty savage, and the elves are xenophobic semi-necromancers (which, again, doesn't automatically mean "evil"). Fantastic Racism is still a thing, of course, but it's no longer a justified trope. Dragons are also no longer Color-Coded for Your Convenience.
Deadlands has this in spades. There are plenty of nasty bugaboos running around in the Weird West. Most of them are pure unadultered evil, but some just want to get on with their lives, and some have volunteered or been strongarmed into becoming Men In Black or monster-hunters. You can even play an undead MIB if you want to.
The Stranger in Terminal Reality's awesome game Nocturne is a prime example.
In CastlevaniaJudgment, Sypha Belnades (herself a witch) spends her time hunting vampires, werewolves, and those who wield Dracula's power. Unfortunately, her targets turn out to be Alucard, Cornell, and Shanoa, all of whom oppose Dracula just as much as she does. The game tried to justify it by having Sypha come from the timeline before Castlevania III: Dracula's Curse began, thus having not yet met or allied with Alucard.
In The Witcher, there are High Vampires running a high-end brothel who drink the blood of customers without turning them and a Batmanesqe, crime-fighting werewolf. Both present conflicts for Geralt, a Witcher, whose sole purpose is to destroy monsters. In the books, Geralt clearly states at a few points that his moral codex does not allow him to kill sentient beings (like vampires, werewolves, and dragons) without provocation or evidence of their evildoings. And Geralt's explanation for why peasants keep believing in monsters imagined by themselves (while still existing in fantasy setting)? They want to know there's something more monstrous than them. It is stated that vampires are simply another race that came there during Conjunction, and that they reproduce 'normally' (blood is only an equivalent of alcohol for them and can be eliminated from their diet completely.) Geralt's definition of "monster" includes humans too. While his silver sword is more suited for slaying supernatural beings and his steel sword is more suited for killing humans, he says that both are for monsters.
The Worgen of Gilneas have a bit of this as well. Most Worgen are beasts, though often cunning ones, while the Gilneans have found a way to retain a human mind. The people of the town of Darkshire, however, still see the Worgen on a whole as monsters to be exterminated, so the Gilnean Worgen who maintain their non-human forms have set up their base some ways away from the actual town and those within it maintain a human form around the locals.
Semi-justified because the town has been fighting the feral Worgen for years, and the Gilneans' new found sentience is fairly new to everyone.
The Scarlet Crusade, a band of zealots who are determined to wipe out the undead, but they also attack innocent people who they suspect as undead, or undead sympathizers, or just kill them to be very sure.
This trope is the central premise of Touhou 12: Undefined Fantastic Object. Player characters whack decent people who only want their saintly leader back.
Shades of this appear in later Mega Man X games; the Maverick Hunters dutifully destroy any Reploid that goes "Maverick", according to their standards...which would be fine, if those standards were limited to those Reploids actively infected with The Virus or deliberately causing grievous harm to humanity and/or Reploidkind. Unfortunately, it seems to encompass any form of resistance against the natural order of things, including otherwise non-hostile acts like peacefully exiling themselves to their own space colony (MMX4) (though Repliforce was implicated in the deaths of several million people and refused to clear their names because it would involve doing things that would conflict with their martial pride, namely disarming and coming in for questioning) or merely having traits that could potentially cause problems with controlling them (MMX6). In fact, it's revealed inMMX5 that the Maverick Hunter commander in charge during X4 retired in disgrace for misapplying the label of "Maverick" on RepliForce, and thus causing the deaths of hundreds of thousands of innocent Reploids. Doesn't stop X or Zero from blowing away their Designated Villain targets, though.
In Runescape, there is a series of quests in which the player helps save pacifist goblins from a group called Humans Against Monsters.
Master Of The Wind plays around with Fantastic Racism a lot, and while vampires generally areAlways Chaotic Evil, the undead are not. So when bad guys decide to remove undead hero Stoic when he becomes an inconvenience, they just tell the Knight Templar priestess/mage Gabriella Robin where he'll be and wait for her to do their job for them.
In Divinity 2: Ego Draconis, the Dragon Slayers have been systematically exterminating all the dragons and Dragon Knights because a Dragon Knight betrayed and murdered The Divine One during a confrontation with Damian, the Damned One long ago. Not only are the dragons mostly innocent of this (the murderer was corrupted and controlled by Damian at the time), but they have been hard at work preventing Damian from destroying the world ever since then, a task not made easier by having an organization dedicated specifically to their personal annihilation.
The Reveal in Nie R shows that the shades, aka "Gestalts", that the player has been killing are far from evil monstrosities. They're the true humans while the humans we've seen are "Replicants", shells initially meant for the Gestalts to bond with once the millennium-long plan to save humanity came to fruition. However, Nier, in his tireless quest to save his daughter, has ensured the extinction of humanity. Worst part is that the Gestalts normally have no way of communicating with the Replicants (who were not supposed to be sentient in the first place) and many of the Gestalts have gone insane.
The Silver Hand, a group that hunts werewolves. It wouldn't be a problem... except they don't make any distinction between werewolves who are a problem and those who just want to live. If that weren't enough, a tour of some of their bases indicates that, when they have a chance, they'll capture a werewolf, torture it to death, and dismember the corpse in order to get every advantage they can against the enemy.
Of course they are also hostile to the player even if they aren't a werewolf, so its likely they are just another group of bandits who happen to focus on werewolves.
Then there are the Vigilants of Stendarr, a wandering order devoted to the Divine of Mercy. They're dedicated to wiping out vampires, werewolves, and daedra - all of whom have relatively non-evil examples in game - both to protect the mercy they believe these creatures loathe, and to grant mercy to those they see as tainted.
Invoked by Serana, who reasons with the vampire hunter PC that they technically could kill her just because she is a vampire, but should not do so because there are eviler forces in motion and she is just trying to understand what's going on.
Vanda Hellsing from Dead Hungry Diner. Initially protecting the town of Ravenwood from zombies by fighting them, when the main characters Gabriel and Gabriella find a peaceful alternative, she's disgusted and starts trying to kill their monstrous customers.
Donovan Baine from Darkstalkers is a monster killer. In the opening to Night Warriors, he is shown targeting, in addition to definite bad apples like Huitzil and Lord Raptor, Felicia. Felicia is a perfectly nice, kind (almost innocent) Cat Girl who is a Friend to All Children. Yet Donovan still wants to kill her.
More explicitly an element of Bulleta/B.B. Hood's character. She kills monsters simply because she's greedy and sadistic, gleefully targeting even harmless fellow cast members for death. Her ending even involves her preparing to murder a pair of innocent wolf demons who are already terrified of her from the monster news reports of her indiscriminate slaughter.
It's practically impossible to kill monsters and not do this in Mass Effect. Rachni seem like just your regular monster, wreaking havoc on the research facility on Noveria, but it turns out they're sentient and somewhat intelligent and plead you not to exterminate them. The Thorian that terrorises colonists on Feros is being an asshole to everyone, but it turns out that's partly because Saren double-crossed it and it no longer trusts anyone. And even the Geth get enough sympathy in the sequel that just shooting them on sight like we'd been accustomed to isn't as justified as we thought.
In the Whateley Universe, there's the ongoing conflict between Carmilla and the Reverend Darren Englund and his student posse. So far, he's been behind at least two attempts on her life. (To be fair, Sara is generally depicted as one of the good guys right now, but it's easy to see why even characters rather less fanatic than Englund might worry that there could be a Face Heel Turn looming in her future — and as she's a budding cosmic entity, that would be decidedly bad news.) Even better, there's a Whateley student named Nightbane. She's an Exemplar blonde and good religious girl whose powers are ideally suited to fighting creatures of the night. She's the bad guy, since she's trying very hard to kill Carmilla.
Carmilla's a descendant of Shub-Niggurath on her father's side and of Cthulhu on her mother's side. She is foretold to be the thing that wipes humanity off the face of the earth and replaces us with her spawn. As The Kellith, she has an evil cult that numbers in the thousands. She has Combat Tentacles as well as Naughty Tentacles. Her closest (only?) living relative is a high-level supervillain known as the Necromancer. If there weren't stories told from her point of view, no one would think the Reverend and his monster hunters were in the wrong.
The SCP Foundation is determined to contain every abnormal being they come across, even if they're completely harmless. One of its rival organizations, the Global Occult Coalition, plays this straighter as they are dedicated to destroying every SCP they can find.
Partly subverted in that "contain" has a flexible meaning based on just how harmless a given SCP is; so for SCP-682, contain means "keep in vat of concentrated sulfuric acid so as to prevent 682 from murdering humanity"; for the tickle monster that once managed to subdue 682, it just means "keep fed and happy".
Some, like SCP-085 (The 2D woman) and SCP-507 (Dimensional Shifter), are quite friendly with staff members. 507 even gets (monitored) internet access.
Others (the every-drink-ever machine) get put in the break room.
The world mostly operates on the convenient D&D Always Chaotic Evil (and Color-Coded for Your Convenience) rules for creatures, but occasionally, questions are raised, especially in the "Start of Darkness", where we see the Sapphire Guard slaughtering a peaceful goblin village and learn the reason why some fully sentient species are Always Chaotic Evil in the first place (hint: gods are jerks).
In fact, most times Redcloak gets a significant portion of dia/monologue with the heroes, he spends time pointing out these kinds of things.
And Shine Heaven Now brings this up a lot, especially when it comes to the difference between Hellsing and their Catholic counterparts Iscariot. They do the same things (on occasion), but for very different reasons.
Exterminatus Now goes so far as to have a zombie shout "HATE CRIME!" at the heroes after they shoot it. That said, this zombie had just been having a conversation with his buddy about how he'd murdered a few of the living (and yet still portrayed himself as the victim), so this wasn't exactly undeserved...
In Sluggy Freelance, Riff has occasionally been cast in this light when it comes to Sam (a vampire) and Aylee (an alien). He cools down on it a little when Torg points out that Riff's own Mad Scientist experiments are just as likely to cause mass destruction and death as any monster.
Goblins: Life Through Their Eyes is built on this trope. It takes place in a universe where the traditionally evil races of D&D are *not* always chaotic evil, but still have their traditional reputation. Enough fantastic racism is in place that the "good" races are perfectly willing to slaughter them now and cast spells that reveal alignment never. To drive the point home, it introduces members of the "good" races, such as Kore, Dellyn Goblinslayer, and Saral Caine, who are amoral at best and far more vile than any characters from the "evil" races at worst. Kore is a paladin who kills a dwarven child because prolonged contact with "evil" contaminated him, and Dellyn's actions sicken even Min-Max, a brainless fighter who (at the time) had no problem killing monsters.
In Scary Go Round, the West Yorkshire Anti-Zombie Unit leap into action when they meet Zombie!Shelley (long story), but soon have the error of their ways pointed out to them. Ashamed, they decide to be a "more caring group, rehabilitating offenders in the community," because "Just because someone doesn't have a soul, doesn't mean they don't have a heart." 
In Slightly Damned, most warrior angels attack demons on sight, due to generations of conditioning from the Great War. Notably the seraph Denevol, who tried to kill "Demons and traitors", aka completely inoffensive protagonists Buwaro and Kieri.
Eerie Cuties and it's spin-off, Magick Chicks, has entire academies of monster-slayers. Bizarrely, while the heads of these schools seem to be on good terms with the principal of Charybdis Heights, no effort appears to have been made to teach young slayers that most monsters nowadays are not ravening, murderous beasts. Granted, when someone like a succubus loses control, things get very dangerous very quickly.
In DMFA, "Creatures" (anything is more innately powerful than the "normal" anthropomorphic Beings — demons, dragons, 'cubi, etc) have not only a well-deserved reputation of being Always Chaotic Evilcannibals (in the sense of devouring other sapient beings), but also a culture that encourages it, to the extent that Beings officially sponser and train adventurers who have a reputation for not always being as discriminating as they could be. While it is true that the exact innocence of the Creatures being killed can be highly debatable, a lot of Creature protestations being based in Moral Myopia, there is at least one reported case of a totally innocent 'Cubi being killed just for her race: Mink's mother.
Doctor Von Goosewing from Count Duckula keeps coming after the titular Count, despite the fact that he (the Count) is a vegetarian (actual vegetarian - not just a Vegetarian Vampire).
An interesting variation of this trope occurs in The Real Ghostbusters. While many of the supernatural entities the Ghostbusters came across were as evil and dangerous as one might typically expect and had to be busted in one way or another, sometimes the ghosts, vampires or other beings were, in fact, the ones who needed the Ghostbusters' help. Whether it was a family of suburban spirits hiring the Ghostbusters to get rid of the malign demons that infested their house, ghosts who were causing trouble for the living but only needed the Ghostbusters' assistance to complete their Unfinished Business to be able to rest in peace, or a clan of vampires that fed on synthetic blood needing help with some overzealous vampire hunters who wanted to kill them even when they weren't a threat, the Ghostbusters could just as easily be helping the supernatural as fighting it.
The first Big Bad in American Dragon Jake Long was an organization called the Hunts Clan, which was dedicated to destroying all magical creatures, especially dragons. The Dragon (who is not an actual dragon) is a girl named Rose, and Jake is both her main target (in his identity as a dragon) and her love interest.
Valerie Gray from Danny Phantom, who is fully convinced all ghosts are evil. Her primary target is the not evil half-ghost hero Danny Phantom. For that matter, the series also has also shown Danny isn't the only good ghost around, but that sure won't stop her!
Similar to the Huntsclan, Juniper Lee had H.A.M. (Human Against Magic), an organization that hunted monsters regardless of their alignment. They're not exactly fond of humans that help them either, a.k.a Juniper (though she is magically enhanced, so it falls under their range of targets).
Happens a lot in Gargoyles. The species was almost wiped out by humans. In particular, there are the Hunters (Gillecomgain and the Canmores) and the Quarrymen (a modern hate-group spawned from the former). The Hunt began because of Demona, who actually is evil, but neither group bothers to distinguish her from all the perfectly normal, decent gargoyles who just want to be left alone. And the massacres had already driven gargoyles to the brink of extinction long before Demona's lifetime.
Ben 10 Ultimate Alien: under the orders of Old George, the Forever Knights are out to hunt down every alien on Earth, regardless of whether they're good or bad. Understandably, it's a lot harder to find the bad ones, so the good ones get targeted. Argit was the only real bad guy they ever harassed. This lasted for one episode; Ben made it very clear that there would be lethal consequences for persisting, and they took his threat seriously. What's really strange is that Old George's command isn't even internally consistent. He has a very specific beef with an all-powerful alien, one to whom the target aliens were in no way related. Indeed, he is shown to not care that his subordinates have failed, which brings to mind the question of why he directed the resources of his organization to a meaningless task when his stated aim is to prevent the rise of one far worse.
Probably to keep them out of his way mostly, it's not like he needed their help. So either he's being a somewhat nice guy (to fellow humans at least) and keeping them out of harm's way, or he knows they'd just get in his way, slow him down and pretty much be problems at best.
Generator Rex: In the episode "The Hunter", Hunter Cain is an EVO-hating extremist who wants to kill every EVO on the planet. Later on, after a timeskip, Providence itself becomes this, catching and putting Restraining Bolt collars on every EVO, no matter their alignment or intelligence.