The Black Knights of Code Geass, particularly Ohgi, fall victim to this when they fall for both logical and moral incongruities put forth by Schneizel to turn them against Lelouch. Ohgi, despite believing that people should not be treated as pawns, nevertheless allows himself and the others to be manipulated by Schneizel in order to get rid of Lelouch. He probably thought of it as choosing the lesser of two evils. In the same scenario, Villetta Nu, while acting out of concern for Ohgi, leaves out a number of details (that she may or may not even have been aware of herself, given that it's likely all her information on it came from Emperor Charles and who knows how honest he was with her) that would have cast a favorable light on Lelouch, namely the limitations of said power, thereby needlessly (or maliciously) hurting the latter's case.
On top of that, Ohgi, who claims that people should never be used as pawns, uses Kallen as one to draw out Lelouch, who he intends to sell out to Schneizel, as yet another, in exchange for Japan. On top of this, for all the complaints of Lelouch going AWOL during the Black Rebellion, Ohgi did the same a few episodes before the current predicament here on account of Villetta. Speaking of which, one of the charges brought against Lelouch is that he's a Britannian Prince, even though no one takes issue with Ohgi's tryst with Villetta, a Britannian agent, one who had been monitoring Lelouch while he was captured no less, and was the one responsible for incapacitating Ohgi in the first place partly due to the latter dropping his guard with her, and that they were taking the advice of not only said agent, but also that of Schneizel, a current royal, and, barring the Emperor himself, the most notorious one at that, whereas Lelouch had been in exile after being tossed away as a disposable pawn and given every reason in the world to loathe the Empire that betrayed him and stood for everything he hated. To top all of this off, such a deal, if it were to go through, would likely result in something tantamount to Lelouch abandoning the Black Rebellion, only magnitudes worse: the Black Knights essentially abandoning their duties as military front of the UFN, and thus their duty of liberating the world from the Britannian Empire.
In Full Metal Panic!, Leonard Testarossa considers himself morally superior to Sousuke because he has never killed anyone. He doesn't even consider how many people have died or ended up in mortal peril because of his deliberate actions, like giving super-mechas to notoriously unstable terrorists like Gauron and Gates. The number of people whose death Leonard has indirectly caused exceeds Sousuke's body count by several orders of magnitude, but Leonard still thinks he's better because he's never killed anyone in person.
The very first story with Catwoman (or 'the Cat' as she was known at first) has Batman sternly Break The Fourth Wall to remind the readers that crooks should never be admired and be fought at every turn. Four pages later he allows the Cat to escape (and deliberately foils Robin's attempt to stop her) for the sole reason that he finds her sexy - other than being a non-violent thief (who still put peoples lives in danger by choosing a scumbag partner when she robbed a yacht) there are literally no other extenuating circumstances in favor of letting her go.
Most absurd version of this (that didn't actually happen)? Spider-Man made a deal with Mephisto. You know, big demon guy? Makes deals with people and then screws them over? The deal in question? He wiped his and his wife's marriage from history, aborting their unborn baby in the process, just so his aunt who, even in terms of comic book aging is older than the Bill of Rights, can recover from a gunshot wound to live for a couple more years before finally kicking the bucket. And to add insult to injury, she only got shot in the first place because Spidey revealed his Secret Identity to the public, making the exact scenario he has been harping about for bloody years as to why he specifically shouldn't take off his mask. In other words, Aunt May was shot because of Peter's mistake and he was unwilling to take responsibility for his actions. And we were meant to think this act is heroic somehow. The Moral Dissonance? Spider-Man just about giving the Devil the chance to fiddle with Reality Warper powers instead of taking responsibility for her death goes completely against the saying "With Great Power Comes Great Responsibility." (The most defining part of his entire character).
Marginal example: Most superheroes in the Marvel Universe don't get along with The Punisher because he kills the bad guys, but are A-okay with Wolverine who does the same thing. Marginal because part of the reason is likely that Wolverine doesn't enjoy killing and usually has a fairly rational reason for doing so (usually either self-defense, in the context of a war, or It's Personal) while The Punisher, if he has any feelings towards the matter at hand, enjoys it and seeks out people to murder as his standard way of crime fighting, but still an example due to both being unrepentant killers (if of significantly differing degrees of moral culpability and dangerousness).
Avengers vs. X-Men: In the end, the Phoenix Five are punished, with Cyclops being regarded as a war criminal. Never mind the fact that they were mind controlled by the Phoenix and shouldn't be held responsible, but many of the people condemning them for their actions have also committed crimes while not themselves, but also Cap's behavior during the whole debacle is very similar to the way Tony Stark acted during Civil War, which Cap was violently against. Add in the fact that the whole mess and every time it escalated was directly the Avengers' fault, making Cap, the Avengers, and the X-Men that sided with the Avengers come off as very hypocritical.
To their credit, Marvel writers seem to have realized this, with Cyclops raising most of those points word-for-word. There is a huge in-universe groundswell of public support for him.
Knowledge is Power: As in some of the author's other works, the canonical "pureblood supremacy is bad" message clashes severely with how the reader is supposed to be cheering for "Lord Potter" as he gleefully boasts about being better than everyone else because he had the right ancestry. Oops.
Boiler Room. In the end, Seth convinces Chris to "do one thing right" and sign a ticket sale making one schmuck client good by stealing from another anonymous buyer on the market.
The fact that Bella is worth fighting for and dying for the Cullens and all the werewolves, but the concept of fighting to stop the vampires from eating anyone else is ignored. She is the only one they are willing to protect, because nobody could ever be as perfect as Bella. Everyone else is considered food whenever their vampire friends from out of town stop by.
She also thinks her father is creepy because he checks in on her at night. Despite the fact that a) he's her father; b) he's a police officer; c) she endangered her life numerous times and his worrying is entirely reasonable; and d) her vampire boyfriend has been watching her sleep before they even started dating and oiled her window frame so that it doesn't squeak.
In the V. C. Andrews book Seeds of Yesterday (the final book in the Dollanganger series) the protagonist Cathy reacts with anger and disgust when she discovers her son and daughter-in-law's adulterous affair (the woman is married to her other son), and when she realizes the extent of her teenage daughter's promiscuity. Meanwhile, she's carrying on an incestuous relationship with her brother and acts as if this is perfectly acceptable and normal.
In David Eddings' The Elenium and the sequel books The Tamuli, we meet Kring, chief of the Peloi, a tribe of savage horsemen. In his first appearance, his troops have joined an allied army to fight a joint enemy. He asks about the army's policy on raping. He is told that it is not allowed and he sighs, saying it will be hard to explain to his men that they can't. Later, his fiancée talks about how she murdered men who attempted to rape her. He clearly shows how he thinks rape is wrong and he is glad they died. No one in the story seems to recall or mention that he was unhappy that his men weren't allowed to rape women earlier. Considering the time period The Elenium is set in, Kring might see a difference between taking a woman as a war trophy (as was commonly done long ago) and men simply setting upon a woman in the night, however. It could also be a case of Moral Myopia where he thinks it's wrong if a woman he cares about is involved, versus the anonymous strangers who he was asking about previously.
In the Dragonlords series by Joanne Bertin, Dragonlords are weredragons born as humans, usually very low class humans, who are considered semidivine by human society. A Dragonlord, talking to a noblewoman, says they're born low class so that when they make judgments on human conflicts they will pick whatever suits the people, commoners included, without regard for noble pride. A young Dragonlord who hasn't yet changed into a dragon - no one but the older Dragonlords even know what she is - is randomly attacked by said noble and almost blinded - and the older Dragonlord characters, upset, consider it an outrage because a human attacked a semidivine being, and it's repeatedly stated that they wouldn't be upset at all if she was the commoner she appeared to be. So rather than following noble pride, they're going on the pride of semidivine beings.
The Souls from The Host consider themselves peaceful, loving, and perfectly moral, despite the fact that their primary activity appears to be wiping out other sentient species (that is, the species still exists in a biological sense, but the individuals composing it are functionally dead. At best, it's slavery on a grand scale, but since what happens to the individuals is closer to murder "wiped out" isn't pushing it too far.)
Star Wars Expanded Universe. Details of the Clone Wars are revealed in the expanded universe to be morally dissonant. The Jedi and the Republic, the good guys of the Star Wars universe, who supposedly outlawed slavery use an army of mass-produced living slaves as cannon fodder for a war in which the soldiers have no stake. Forced into live-fire training, killed if they didn't meet the standards of the cloners, and deprived of even names—all between the ages of 2 and 10, before the war even starts. When the fighting begins, they're given no civil rights, no citizenship, no legal standing at all in the society they're fighting for, they're aging twice as fast as naturally born beings, and if they're too injured to continue fighting, they're left to die or euthanized. They were bound to serve for life or until old age inhibited their ability to fight, and any attempts at desertion were met with an assassin squad.
This was commented on multiple times in the Expanded Universe; the Clones had people fighting for their civil rights, citizenship, and legal standing in the Senate. Palpatine always obstructs them, however, and gets REALLY pissed when his attempts to create more cannon fodder are shot down. After all, clones getting equal rights would've disrupted his whole "use a cloned army of Manchurian Agents to wipe out the Jedi" plan. One comic had a group of horrified Jedi meet to find a way to end the war after they discover that the clones view themselves as cannon fodder. Palpatine sends an assassin to kill them.
In Doctor Who, the Tenth Doctor deposing Prime Minister Harriet Jones in "The Christmas Invasion":
The Doctor himself is perfectly capable of committing mass murder against hostile alien species, has done so on numerous occasions, and would continue to do so.
In deposing Harriet Jones, the Doctor is violating his own often stated moral standards of not interfering with major historical events or "fixed points in time" as they're called in this series. We had it on no less authority than the Doctor himself, that Harriet Jones was supposed to have three successful terms as Prime Minister and lead Britain into a Golden Age. That sure as Hell sounded like a "fixed point in time" if there ever was one. Furthermore, everything that's happened since then in the Whoniverse in regards to the British premiership— such as Torchwood's Brian Green— indicate that the Doctor didn't just change history, he also changed history for the worse.
In several incarnations the eponymous heroes are told (or even have it be part of their song lyrics) to only use their powers for defense. This explains why they never use the Megazord to stomp the monster before it grows (they won't risk the property damage until the enemy forces their hand) or why they never directly attack the villain's base (although they did so in Dino Thunder after they found it's location; guess Tommy'd become Genre Savvy). However, there have been more than a few occasions where they blew up the monster while it was helpless and in some cases practically begging for mercy. There's one particular instance in MMPR where the Red Ranger seems downright sadistic...
Jason: Give up, birdbrain!
Monster:(terrified squawks and "I surrender" gestures)
Jason: Then we have no choice! (kills the monster)
In Power Rangers in Space, the Megazord goes completely medieval on Monster of the Week Clawhammer, who was attacking them, to be sure... but maybe ripping out his tendrils, kicking him repeatedly in the groin, and throwing him into lava was a tad excessive. Maybe whatever Clawhammer had done in the Super Sentai episode the fight footage came from was a lot more evil than his Power Rangers actions of simply being a literalGiant Mook. Even worse, Clawhammer was just a mindless alien predator that didn't even work for Astronema. Sure, you could blame Astronema for siccing the creature on the Rangers, but in the end, it was just someone who was dragged into the fight against its will. (In the Sentai version, the corresponding monster was created by the main villains, and was killed by being thrown into a volcano because he was made of a metal their weapons couldn't penetrate)
Later series have the Rangers being more likely to chase down and kill fleeing monsters that the original Rangers would have allowed to pull a Villain Exit Stage Left. Strangely, Power Rangers RPM isn't one, despite the higher consequences of letting a bad guy go free.
A horrible case in Power Rangers Wild Force. There Animus actually takes the Wild Force Zords away because humans have polluted the planet (ignoring that the Orgs would probably win because of this and make the planet even worse). He does give them back eventually, claiming that it was a test for the Power Rangers but that ignores the fact that the Rangers had already been fighting the Orgs for quite some time before Animus did a thing to help them.
In season 2 of the original series, Bulk and Skull's efforts to learn the Rangers' identities result in several occasions of the heroes being complete dicks to them, maliciously destroying any evidence they got.
Minbari do not lie, being such an honorable, morally-superior-to-humanity kind of race. To get around this, they've made an artform out of evasiveness and stretching the definition of truth to the breaking point. They will lie to help another save face, so they could in fact lie all they want as long as they can come up with a vague justification (like the Minbari who lied to help implicate Sheridan in the murder of another Minbari).
The Vorlon and Shadows, whose ships are powered by Moral Dissonance, to the point that they no longer even remember why they're doing what they're doing. That is, until they get called out on it.
In the Blake's 7 episode "Gold", the Seven decide to steal some gold from the planet Zerok, which isn't even part of the Federation (okay, they trade with them but that's stretching the point). In the process, they are responsible, directly or indirectly, for the death of at least fifteen security guards who were just doing their job, one of whom actually had his weapon lowered and could easily have been taken prisoner. Then, their ally Keillor kills a doctor who was trying to raise the alarm and they all treat this as a heinous crime. The stated reason that he wasn't armed doesn't really hold water. Apparently the moral is it's okay to kill innocent bystanders if they're carrying guns.
Smallville is undoubtedly so full of them that one could spend hours yelling at the TV in frustration of Clark's repetitively poor and self destructive decisions. For example, he will often lecture other heroes, or Lois, or earlier Lana, on how important honesty is, and in the case of the heroes, encouraging them to unmask themselves to their significant others, while causing huge problems and creating danger out the wazoo for his own while protecting his own secret. The entire Superman franchise is founded on this, however.
Apparently, it is not okay for Chloe to protect Clark's secret from Lana but it is okay for Lana to lock her into a freezing cellar to trick Clark into revealing his powers. She doesn't even know that he has Super Strength. She only witnessed his invulnerability (and she isn't even sure what she saw). She also does a lot of other stuff like holding Lionel captive, spying and almost killing Lex. Seriously, the only thing that stops her from being a complete unsympathetic villain is that Lex isn't exactly a nice person. She is still portrayed as Clark's perfect girlfriend.
Lionel is supposedly a good guy after Transference, but he still does a lot of morally debatable, if not outright despicable things. Like threatening to kill Clark to make Lana marry Lex. And building an adjustable kryptonite cagefor perfectly innocent intentions.
On VH-1's I Love New York, it's unforgivable to say something horrible about New York's mother Sister Patterson, but it's perfectly fine for her to insult a contestant's family members! There's a reason why Tango dumping her at the reunion show (because she insulted his mother, no less) is considered a Crowning Moment Of Awesome.
There's an episode of Star Trek: The Next Generation in Season Two, in which a population of clones is dying out from a lack of genetic variation in their people. They ask if they can use the Enterprise crew to make clones to help them expand their population but when the entire crew refuses, they drug Riker and Pulaski and create clones of them anyway. Awful though this is, when Riker and Pulaski find the room with their growing clones, they calmly murder them all without the slightest moral qualm. These are living, if-not-yet-aware-and-sentient beings, but no one calls Riker or Pulaski out on this, despite the fact that she is a doctor and (you would think) therefore should do no harm. Immediately after that, they force the clones to marry a group of Irish colonists from another world by threatening to take away their cloning technology on the grounds that the clones need to relearn sexual reproduction and the two groups can provide "breeding stock" (yes, those are the words that Pulaski uses to describes these people) for each other.
Janeway of Star Trek: Voyager regularly ran into this, since Voyager's disregard for consistency meant that her moral perspectives were prone to change, often radically, Depending on the Writer. More than once, she would chew out crew members for morally ambiguous decisions that she would equal or exceed only a few episodes later. Even Kate Mulgrew had no idea how her character's mind worked, leading to her proposing at one point that Janeway suffered from some kind of bipolar disorder.
So, it's wrong to discriminate against people based on race, ethnicity, even species, but legally enforced discrimination against genetic augments is okay because a bunch of them were vicious dictators on parts of one planet several hundred years ago? How does that work out? Ask the guy who wrote DS9: "Dr. Bashir, I Presume".
The BBC's Robin Hood often insists on a "no-killing" policy, telling his allies and enemies alike that he only kills people when absolutely necessary. This... is rubbish. By the end of the series, he had needlessly shot countless guards (often in the back), a mentally-deranged man who was holding his friend hostage (this was after trying to kill him earlier in the episode whilst he was unconscious), and a corrupt churchman who wasn't doing anything more threatening than just standing there making bitchy comments. The worst example is when he barges into a woman's bedroom to find that she's just killed her sadistic husband in self-defense. He grabs her around the throat and accuses her of murder, literally minutes after shooting dead an executioner who was just doing his job. The fact that the show had long since established Robin as a flawless archer means that all of these deaths could have easily been non-fatal injuries if he had so chosen.
The moral framework of Merlin was convoluted to say the least. Essentially, the show’s core conflict pitted an oppressed magical class against the powerful kings of Camelot, who enforced a genocidal regime against all those who practiced magic. The setup is that the protagonist Merlin must secretly use his magic to protect Arthur, The Chosen One who is destined to reign over a fair and just Camelot. Merlin gets this information from Kilgharrah, a prophetic dragon that Uther has chained up in the dungeons, who promises him that Arthur will lift the ban on magic and free Merlin’s people once he’s king. In light of the Grand Finale, two major problems emerge from this premise.
1. The fact that Merlin blindly takes orders from the morally ambiguous Kilgharrah gets more and more exasperating at the series goes on. Among other things, the dragon holds back on vital information that nearly results in Merlin’s mother’s death, guns for the deaths of Mordred and Morgana before they’ve actually done anything wrong (and whose condemnation of them partially results in them becoming the antagonists that he initially warned Merlin against) and who at one point lays waste to Camelot once he’s freed from his chains, killing at least seventy-six people, and even taking a near-fatal swoop at Arthur.
Now, this wouldn’t be Moral Dissonance if Merlin acknowledged all this and cut ties with the dragon, but the bizarre thing is that no matter what Kilgharrah says or does, Merlin (and the narrative) continues to treat Kilgharrah as a font of wisdom and good advice. Even when his prophesies are flat-out contradicted by events, or when he clearly manipulates Merlin into doing something against his better instincts (which always leads to disaster) it’s simply ignored by Merlin, who continues to trust that Kilgharrah gives him sound information and guidance, calling him "old friend" on more than one occasion.
2. Despite all of Kilgharrah’s prophesies that Arthur would be The Good King who lifts the ban on magic and allows everyone to live in peace and harmony – he’s not. Merlin and Arthur never actually get around to legalizing magic, much less integrating magic-users back into society, rendering all of Kilgharrah’s prophesies/Merlin’s efforts null and void. What we end up with is a hero who – instead of fighting the oppressive, genocidal regime he lived in – spent ten years actively supporting it, eliminating any threats to it, and protecting the two people who enforced it, in the hopes that one day things would get better simply because a manipulative, deceitful dragon told him it would. Since it doesn’t (at least not under Arthur’s reign, it’s confirmed by Word of God that Guinevere handled things much better after Arthur’s death), then all of Merlin’s methods in protecting Arthur and Camelot’s anti-magical stance are thrown into a highly questionable light.note This includes manipulating people, consistently lying to loved ones and keeping back vital information, making crucial decisions on behalf of other people without their knowledge or permission, killing in order to keep things a secret, regularly throwing fellow magic-users under the proverbial bus, unleashing a powerful magical force that kills dozens of innocent people, using magic to brainwash people into acting against their will (and deriving enjoyment from it), making pre-emptive strikes against individuals who have yet to threaten them in any way, murdering in cold blood, and remaining single-mindedly devoted to a dubious cause on the insistence of an equally dubious mentor-figure — in other words, everything that Morgana, the show’s Big Bad does. Also baffling is that Kilgharrah waxed lyrical about Arthur’s destiny as a fair and just king, even though he didnt end up doing anything to improve the lot of magical folk, whilst simultaneously condemning Morgana as an evil witch, even though she was initially fighting for magical rights and was desperate to remove Uther from the throne – two of Kilgharrah’s own goals. You can’t help but feel that Kilgharrah was betting on the wrong horse, even though his frequent warnings to Merlin about Morgana’s imminent evil only resulted in Merlin isolating Morgana — one of the key factors in turning her against Camelot in the first place.
Season 5 of 24 has Tony Almeida attempting to kill Christopher Henderson, the man who'd earlier ordered the death of Tony's wife Michelle, and Jack is repeatedly trying to talk Tony down from doing it, saying he's going to get nothing out of doing it and he'll just be left empty, and of course since Jack is the main character he's supposed to be the one everybody should be siding with. It would have sounded a hell of a lot better if it wasn't for the fact that this is coming from the same man who's repeatedly had no problem killing someone in revenge, times including the Drazen family, Nina Meyers, the guy who assassinated David Palmer just a few hours before, and ironically Henderson himself later on in the season. They do need Henderson alive since they need to discover who he's working for in the current conspiracy of the season, and admittedly Jack at least does put his desire for vengeance on hold when said person he wants to kill is still needed by CTU to accomplish something in stopping the greater terrorist threat, but this is never brought up. The dialogue simply has Jack stating that revenge isn't the answer, which makes him come off as nothing but a total hypocrite.
Sometimes, there's a moral double standard concerning faces and heels where faces can get away with things heels would be condemned for, such as assaulting non-wrestlers and cheating, even outside of the confines of the "Well, the heel started it" justification. A good example was at Backlash 2000 where The Rock and Triple H used very similar tactics but where Triple H was lambasted by Jim Ross on commentary for it (such as when he low blowed the Rock), the Rock was more or less given a pass whenever he skirted the rules (like low blowing Triple H) as acting "in desperation".
It's A-OK for Hornswoggle to get involved in other people's matches and wreck other people's stuff but when the heels finally put the little punk in his place we're supposed to believe they're the bad guys. Made even more disturbing when he interfered in that 8-diva tag match. He was trying to drag Laylaunder the ringand presumably have his way with her. Michelle saving her friend from getting raped by a leprechaun should get her a medal.
One Raw found Triple H at the mercy of Lance Cade and Trevor Murdoch, when Brian Kendrick and Paul London (who were feuding with Cade & Murdoch at the time) ran out to rescue Hunter. How'd he repay London and Kendrick for the assistance? Pedigreeto each of them, and the commentators just laughed it off and said they had it coming.
The Bella Twins switching before their Face-Heel Turn. The announcers called it "twin magic" and it was treated as fun and whimsical. Their feud with Jillian started because they pulled the switch on her in a match, unprovoked, yet Jillian was meant to have deserved it somehow.
Current Raw General Manager A.J. Lee is this trope cranked Up to Eleven, so much so that it's starting to come off as a Karma Houdini. A.J. emotionally manipulated CM Punk, Daniel Bryan, and Kane for weeks, breeding partly needless animosity between them and putting their lives in danger at one point. She also accepted Daniel Bryan's marriage proposal, only to reveal at the last minute that it wasn't going to happen. Now that she's in charge of the entire Monday night program, she's continuing to do much of the above plus acts as a petty tyrant who is constantly putting wrestlers she doesn't like (admittedly, theyareheels, although it doesn't mean what it used to) into painful or humiliating situations just because she's offended by the word "crazy" (which these characters don't always use to refer specifically to her). Even CM Punk has begun calling her out for this behavior, only for the other "good" characters to simply dismiss him or call him out in turn. Through all of this, A.J. has remained a de factoFace, with all of her Jerkass tendencies being handwaved as just A.J. being her naturally quirky self.
It's egregious enough that WWE.com has an article asking if she's unstable or power-hungry. Said article even singles out another fault. The night after SummerSlam, AJ booked a rematch between Dolph Ziggler and Chris Jericho, and decided seemingly on a whim to put Ziggler's World Heavyweight Championship Money in the Bank contract and Jericho's job on the line. This was bad enough without adding, as the article does, that she told Alberto Del Rio earlier in the night that she couldn't name him #1 contender for the World Heavyweight Championship because she didn't have jurisdiction over that title, as that was Booker T's territory on Smack Down. Dolph won the match and Jericho went back to Fozzy, but AJ overreaching and almost screwing Dolph out of his dream chance was enough to rile up Vickie Guerrero, who never liked her in the first place, into campaigning to get her fired.
In a backstage segment on SmackDown in late 2007, Kristal Marshall was planning her wedding to General Manager Theodore Long and telling Torrie Wilson and Michelle McCool that she had chosen them as bridesmaids. Then Victoria (who was a heel for most of her WWE career, but highly respected by the fans for her wrestling prowess) showed up and expressed joy that she, too, might be maid a bridesmaid. Mc Cool promptly told Victoria that nobody would ever let her be a bridesmaid, which seemed excessively cruel. What made this worse were the Unfortunate Implications involved: Victoria could have already been seen as an outsider due to her large size (making her "fat" and "ugly" in the eyes of more petite Divas) and dark, vaguely "ethnic" appearance (part Turkish, Puerto Rican, and Italian, while Wilson and Mc Cool are both blondes and even Marshall, who's black, has relatively light skin and almost blonde hair), making Mc Cool's bullying arguably not only sadistic but a form of coded hate speech.
One particular example in World of Warcraft tends to portray graverobbers as villainous, but the players robbing the corpses of freshly killed soldiers, and in some cases, civilians, is considered OK.
Of course the guys (Consortium Ethereals) sending the players to kill said graverobbers (Shaffar's Ethereals) are outright graverobbers themselves and are blatantly stated to be sending the players to eliminate the competition. Additionally, at least one graverobber hangs a lampshade on the double standard:
Adventurers are such hypocrites! Like YOU just FOUND your weapon on the side of the road!
Dragon Age II, the player has the option of hunting down mages or diplomatically talking them into returning to their confinement; equally unfortunately, the option to actually free them only appears once or twice. Hawke is either a mage or sheltering his/her mage sister through most of this. The dissonance is probably intended, and Hawke does get called in this by Anders if s/he is a mage and is opposing Anders' efforts to free mages.
It has two side quests where you can help people with romantic complications. In Girdershade, Ronald Laren wants you to get him a full case of Nuka-Cola Quantum so he can wow his neighbour Sierra (a nuka-fan and apparently addict) and (he hopes) convince her to put out for him. This gives you bad karma. In Rivet City, Angela has the hots for young, celibate acolyte Diego, who likes her but really has his heart set on becoming a priest. To "help" them, you have to provide Angela with pheromones which will make her irresistible enough for Diego to do the dirty deed with her... and once it wears off, he's kicked out of the priesthood and married off to a woman who practically date-raped him. Your helpful assistance nets you good karma. Cue Double Standard: Rape, Female on Male.
There's also the Tenpenny Tower mission. Roy Phillips is being denied permission to buy an apartment because he is a ghoul, and Alistair Tenpenny hates ghouls. As he storms off, Phelps makes various death threats against Tenpenny, and one of the three solutions to the quest is helping him murder everyone in the tower by unleashing a horde of ghouls into the building. The main reason the inhabitants don't like ghouls is because they think they're all mindless, murderous zombies, which is perfectly justified by Phillips' reaction. Similarly, even if he weren't a ghoul, he's willing to murder everyone in the tower (which includes the Retired Badass and kindly old man Herbert Dashwood) because they wouldn't let him buy/rent a room. For each of the other solutions, you convince the tower's inhabitants to give Roy a chance, and they let him in and give him a room... a few days later, he's murdered all the human inhabitants, and proved their bigotry right again. And if you kill this man who has proven himself to be a psychotic murderer, Three Dog declares you to be a monster and a bigot.
As Yahtzee points out in his review of Dead Rising 2, the game refers to one of its main antagonist groups as "looters," but at the same time, the player is encouraged to break open ATM machines and acquire wealth to buy Zombrex (from those same "looters").
A particularly infuriating example in Chrono Cross: early on, you hear about the dwarves inhabiting Hydra Marshes in Home World. Later on, the Hydra is killed by humans, which kills the marshes and drives the dwarves out. Some time later, your party goes to Water Dragon Isle and discovers the dwarves are slaughtering the fairies to give themselves a new home. When you finish off the dwarf chieftain, he calls Serge out on the death of the Hydra, asking why humans can't just live in harmony with other species - never mind that the dwarves just massacred the fairies!! One dwarf actually says: "You do not cherish the treasures of nature as we do!" while the ground nearby is littered with the corpses of the fairies they just slaughtered. After you stop the dwarves, do the surviving faeries thank you for saving their lives? Nope, they blame the whole mess on humans for having driven the dwarves out of their swamp in the first place, as opposed to the dwarves who were committing genocide for the sake of stealing someone else's lands. The dwarves even give their big speech about nature, immediately after their battle tank is defeated by the party.
In Touhou: Embodiment of Scarlet Devil, when Rumia points out to Reimu that she had seen humans working at night, Reimu explicitly says to Rumia that she can have them for dinner if she really wants. That's not really hero-like since Reimu's job is about fighting youkai to protect humans.
Star Wars: The Old Republic : When Jedi become player characters in an MMORPG, a certain amount of Moral Dissonance is probably inevitable. Yoda said that a Jedi would use the Force for knowledge and defense, never for attack, but in Star Wars: The Old Republic, one routinely sees Jedi hunting down and slaughtering beings that pose no threat to them whatsoever, just so the Jedi can gain experience to advance to the next level.
In Beast Wars, when Blackarachnia eventually joins the Maximals, she strenuously objects to having her Predacon shell program removed on the grounds that it would make her something other than what she is. Come Beast Machines, she herself reformats the Vehicon general with Silverbolt's spark despite him giving the same objection. He doesn't take it well. Though these two things sort of explain each other. Blackarachnia still has Predacon programming, thus allowing her to be an unrepentant Hypocrite. She wants Silverbolt back so she's going to get him back (there are numerous other issues that also cloud the whole thing, such as whether Blackarachnia was self-aware before she was reformatted as a Predacon, while Silverbolt was undoubtedly a person with a personality before being reformatted into a Vehicon.)
In "Toilet Paper" the boys feel guilty about letting Butters take the blame for what they did. They have no such qualms in "The Tale of Scrotie McBoogerballs" when they attempt to blame Butters for writing the book when they think it'll get them in trouble and when they blame Sarah Jessica Parker's death on him.
In "The Biggest Douche in the Universe" John Edward is declared a douche because he is holding back humanity's progress through false hope and lies and telling people how to live their lives. Yet one season later in "All About Mormons" Stan is declared an asshole for insulting Gary's religion which he himself admits is likely false on the basis that it provides good moral lessons.
Larry: You can't just kidnap people from history and treat them like some kind of pet!
Tuddrussell: Well, what about Otto?
Larry: Ooh... Well, you can't keep kidnapping people from history...
Danny Phantom has polarizing eco-feminist Sam Manson tell Danny he should use his powers to do good things and not hurt others...only to tell him he should use his powers to haunt a car lot so people won't buy ecologically unsound trucks. Danny doesn't do it, but no one calls her out on it.
The second season premier of Loonatics Unleashed has a battle near the end where the villain sneaks up on Ace Bunny and jump-kicks him from behind, with Ace calling him out on it. A couple minutes later, Ace takes advantage of the villain's distraction to jump-kick him in the back. Made worse by the fact that this battle is supposed to be proof that Ace is a "true warrior" (i.e. better than the backstabbing villain) and worthy of the Cool Sword at the heart of the episode.
In the Hero Factory episode Invasion from Below, Hero Natalie Breez discovers that the beasts are only attacking the city because a drilling operation has disturbet their nest, and that they are actually sentient, sapient beings. After Breez makes peace with them, a stray gunshot fired by an stepped-on weapon causes the beasts to attack again. This time, the Heroes don't bother with reasoning, instead they kill them all, unhatched eggs included. The end of the episode finds our Heroes celebrating and being celebrated, with Breez joining in on the party.
Admittedly, not THAT much dissonance in Pichas adult comedy "The Big Bang" when the intergalactic hero who was sent out to stop nuclear war on Earth pushes the red button himself for scorned love. Since that "hero" is a complete twit, we almost expected something like that coming...