Iron Man during Civil War, with Captain America as the Designated Villain, Depending on the Writer. In some issues from that arc, the exact opposite effect occurred: Iron Man appeared to be the Designated Villain (to many, he seemed like a reasonable guy defending normal humans against powerful forces while trying to avert a backlash against superheroes, yet some writers expected us to root against him) and Cap seemed like the Designated Hero (refusing to take seriously Iron Man and Reed Richards' arguments that humans were in danger due to the mega-powerful supers running loose and unaccountable, yet some writers expected us to find Cap to be completely reasonable). The fact that the writers themselves seemed to be fighting over which side was right just added to the confusion; some sources claim that there wasn't actually a single, mutually-agreed version of the letter of the Super Registration Act, which surely cannot have helped.
Perhaps the Aesop was that neither extreme was truly moral. If that's what they were going for, designated heroes were the way to go. Captain America was the Designated Hero more often than not with Iron Man as the Designated Villain. Mainly because the politics associated with Cap's side tended to resonate better with most of the writers. But all in all, it was a case of a complicated issue being "simplified" by having a good guy and a bad guy. Iron Man and his pro-Registration side all took a big hit in the credibility department when they started tossing anti-Registration heroes into a parallel universe prison without trials.
According to Word of God, the official stance is that Iron Man and the Pro-Registration side was meant to be the one in the right; and they thought it was "so obvious" (despite "Registration" in Marvel comics historically relating to "Mutant Death Camps", and despite Captain America traditionally being the moral compass of the Marvel universe) that they threw in a few Kick the Dog moments to make it seem more ambiguous. If so, they went seriously overboard, since the Pro-Reg does things like try to arrest Cap by force for breaking the Act before the Act was even passed, creating a clone of Thor that went Ax-Crazy and killed an Anti-Reg C-list hero (Bill Foster/Goliath), hiring supervillains to capture their opponents (and giving the Ax-Crazy mass-murderer Norman Osborna major position in SHIELD), throwing captured heroes into a prison without trial in the NEGATIVE ZONE (an otherworldly post-apocalyptic dimension populated entirely with dangerous aliens and monsters) and trying to start a war with another nation (Atlantis). The worst the Anti-Reg side did was hire The Punisher (then fire him immediately), fight Pro-Reg forces, and be on the receiving end of Straw Man Political journalism. The majority of readers sided with Cap and supporters of both sides thought Iron Man was a dick in this story and believed he was meant to be the bad guy.
And then he and Reed Richards (two of the heads of the Pro-Registration faction) use science to make everyone forget Spider-Man's secret identity so he can continue being a vigilante without having to deal with accountability in One Moment in Time. Which pretty much goes against what they fought the entire Civil War and committed all their crimes against humanity to put a stop to. So you can add horrific levels of hypocrisy to the list of what makes them designated heroes.
There was a lot of this in Avengers vs. X-Men as well. Depending on the Writer, Captain America and the Avengers are a bunch of fascists jerks to the plucky underdog X-Men, or Cyclops and his X-Men are a bunch of religious fanatics and dictators waiting to happen.
The aftermath is just as confusing with regards to this trope. Cyclops is definitely framed as being in the wrong (it was him who killed Professor Xavier, after all), but the validity of this is pretty questionable considering why he killed Xavier and that he was spurred on by the Avengers, but other issues have members of the Avengers calling out Tony Stark over his role in the crisis. The fact that the Avengers were the ones to man up and offer the olive branch to the X-Men just confuses the roles even more.
Throughout the series and aftermath, the only one who seems to be constantly a Designated Hero is Wolverine, who essentially causes the conflict by telling Captain America what essentially amounted to biased accounts on Cyclops' character and the Phoenix as a whole, repeatedly attempts to kill Hope because 'it's the only way' to stop the Phoenix (which would have fucked everything up had he been successful), and afterwards doesn't even try to help the newly appearing, and vulnerable, mutants. He does however, find the time to harass Cyclops at every opportunity when he tries to do so.
Things become more complicated and worse when it is revealed Mary Jane egged him on and her reasons why.
Civil War II gives us Captain Marvel, following in the footsteps of Iron Man in the first Civil War and who went a little crazy with her methods while using an Inhuman precog, Ulysses, to combat crimes. She went around trying to arrest her allies and others for things that haven't happened yet, and ignored people when they tried to tell her that the precog wasn't really seeing the future, at least not with 100% accuracy. Having indirectly caused the deaths of War Machine and Bruce Banner, she grew more stubborn in her beliefs and went on to imprison an innocent woman, tried to arrest Miles for a crime he may not commit, and put Iron Man in coma when he opposed her. This was explained in The Ultimates (2015) partly as having her Go Mad from the Revelation of the Marvel Universe's floating timeline thanks to Galactus showing her. While some fans still love the character, others are unsure that she should be the female face of Marvel.
Several years on, thanks to a successful film and appearance in another, a number of negative consequences for Carol and a fair amount of self-hatred on her part, plus a general desire by Marvel to forget that Civil War II ever happened (unlike the first Civil War, which had extended consequences right up to and after Siege), which was helped by how it was a forgettable event to begin with, and Ulysses himself hasn't been seen since - means that it's simmered down to the occasional mention.
Inhumans vs. X-Men has the Inhumans, who are trying to stop the X-Men from essentially saving their people from being gassed by their Terrigen Mists, all so they can continue using those self-same mists to forcibly convert people with Inhuman ancestry into new Inhumans. Needless to say, having people die for their own benefit isn't heroic. And it only gets worse when supplemented by Death of X and the tie-in volumes of Deadpool and the Mercs For Money, both of which prove that to the Inhumans, the Terrigen Clouds are so sacred that they outweigh mutant lives in their eyes. It gets so bad that, when Kamala Khan and other Nuhumans get involved and they find out what's going on, all she can sputter out is "You guys, who are the good guys?" Which by itself is troubling enough because it seems to imply that there is some level of moral ambiguity in the situation, instead of mutants fighting back against genocide (something summed up when Magneto - a Holocaust survivor - roared, "I will not allow my people to be gassed again!").
In the Death of X, it's revealed that Black Bolt executed Cyclops for the hideous crime of... altering a Terrigen Cloud to still function as it should whilst no longer being lethal to mutants. Although Inhumans vs. X-Men tried to retcon that this caused the Cloud to destabilize and fall apart, that wasn't presented as being the case in Death of X, and it still presents Black Bolt in a terrible light, since he still executed someone.
In Deadpool and the Mercs for Money, meanwhile, the characters visit an Alternate Universe where the X-Men had one of their Reality Warpers successfully transmute the Terrigen Clouds to be harmless to mutants and still function to power-up Inhumans. The result? The war between the two races got worse, as the Inhumans were outraged that the Terrigen Mists were no longer 100% the same chemical makeup as they had always been.
This is even more obvious when one looks at the prior history of the Inhumans, which made it clear that they were largely Anti Heroes at best; the noble class of an intensely stratified and isolated monarchy with all the problems that comes with it, including archaic rituals, intense xenophobia, imperialistic ventures, and even slave labor at points. Trying to switch them to being straightforward protagonists was really never going to work.
In their latest incarnation, the Runaways seem to be hitting this trope, as their efforts to reunite the team wreak havoc on the lives of the individual members, with Victor being resurrected against his will, Karolina getting dumped by her girlfriend, and Molly becoming estranged from her grandmother (who is, to be fair, a Mad Scientist, but was still genuinely devoted to providing a good home for her granddaughter.) This is perhaps most pronounced in issue #11, where the Runaways barge in on Klara, who's been Happily Adopted, and try to pressure her into returning, even going so far as to baselessly accuse her adoptive dads of being supervillains.
Some readers feel the X-Men as a whole have hit this point during X-Men (2019). To wit, after years of being the punching bag of... everyone, mutants have founded their own country known as Krakoa. This country quickly becomes a destabilising presence in the world, as its miracle drugs (which have effects including curing incurable diseases and extending lifespans) have a huge impact on global politics and the economy, but are only given to those who ally with Krakoa, which means recognising it as a country and allowing mutants to leave to join it no matter their previous crimes — Krakoa bills itself as a "fresh start", so no crime prior to a mutant joining "counts", meaning mass murderers like Sabretooth and Apocalypse are given free passes. Anyone who attempts to arrest or detain a mutant who is aligned with Krakoa — even heroes like the Fantastic Four — are rebuked and basically told "this is a mutant problem, fuck off" and the mutants will deal with the criminal themselves, without revealing the world how they dealt with it, which does not build trust at all. They also do not allow any humans to visit without supervision. Finally, what laws they do have that seem good, such as the rule against killing any human, have been broken a lot, to the point that most of the high-ranking X-Men know it's just for show and won't be followed when push comes to shove. The books do paint the X-Men as somewhat morally grey now, but for some readers, it's not often enough given the things they're doing.
Spider-Woman begins her 2020 comic book run by throwing a teenager off a boat for talking bad about her. While kid is obviously a jerk, he's also, y'know, a kid. Add this to her sour attitude, even towards people she barely knows, and Jessica comes off as more of a bully than a superhero. This at least gets the justification that her physiology has been sabotaged, causing her to become increasingly and randomly volatile, culminating in her viciously lashing out at all of her friends during King in Black.
