J. Michael Straczynski's Marvel Comics maxiseries The Twelve contains an In-Universe example. Golden Age hero Dynamic Man sees a woman who's been mugged being chased by a black man. Upon grabbing the black man he finds out that this is the victim's husband. He instantly loses interest in helping either one. Likewise, when he helps out a bar that is being attacked, only to realize it's a gay bar, he disgustedly comments that this sort of thing should have been stopped a long time ago before flying away.
The whole series examines the dissonance between Golden Age heroes and the modern world they've found themselves in; while all of them suffer to a degree, Dynamic Man is a particularly ironic example given how he constantly stresses that he's "the Man of Tomorrow".
In his earliest appearances, Black Panther was often called "Jungle Man" by Hawkeye and Goliath. While the name was in reference to his beast motif (and the fact that he literally lived in the jungle), calling a black man that name would justifiably be considered highly offensive in the 21st century. Quite a few people didn't think it was appropriate in the 20th Century.
Likewise, the Black Panther villain who used to be his Arch-Enemy, M'Baku the Man-Ape, has become increasingly sidelined due to the fact that caricaturing Africans as apes or monkeys was quite popular throughout the first half of the 20th century. This makes a big burly African man who dresses up in a gorilla costume and calls himself "the Man-Ape" very inappropriate these days.note When the Marvel Cinematic Universe got around to featuring M'Baku in Black Panther (2018), the gorilla theme remained associated with his tribe and he briefly wears a bit of gorilla themed wear for a Trial by Combat early in the film, but he would undergo Adaptational Heroism and never call himself Man-Ape. Lampshaded in the 2nd volume of Thunderbolts, where the African-American Elemental Shapeshifter Coal has to temporarily disguise himself as M'Baku and complains about the racism in making the black guy dress up like an ape.
If M'Baku is bad, then the C-list mutant supervillain The Mandrill is worse. First, there's his backstory; his father was exposed to radiation at the same time as an African cleaning woman, and as a consequence, the Mandrill was born with black skin and excessive body hair, resulting in his father believing his wife had been unfaithful, a condition that worsened as the kid aged until he literally transformed into a humanoid mandrill in his teens. Secondly, there's his power: he secretes mutated sex pheromones that act as More than Mind Control on women - and only women - by acting as an addictive super-aphrodisiac. And he's explicitly confirmed as a misogynist who shamelessly abuses his powers to get anything he wants from women, including sex. So, in other words, he's a black mannote yes, genetically he's Caucasian, not African, but nobody can tell who is literally a humanoid ape, and whose power-set is, effectively, "super-rapist"note he does also have enhanced strength, reflexes and agility, which fits his ape-man body, but everybody just remembers the super-rapist pheromones. Needless to say, Marvel generally wants to pretend that this guy never existed, although he has popped up in some surprising places — including The Avengers: Earth's Mightiest Heroes and, most notably, M.O.D.O.K. (2021). (They mostly get around it by not discussing his origin and just treating him as "monkey guy with mind-control powers.")
UltimateCaptain America is another in-story example. In order to maintain his World War II origin story for stories in the 1970s and beyond, the original Cap was said to have been frozen in an iceberg and thawed out years later. The Ultimate version goes into depth about the kind of culture shock that would happen if a man, frozen in the 1940s, actually woke up in the 2000s.
Unfortunately, Ultimate Cap actually doesn't feature enough values dissonance. At one point, when talking about possibly surrendering, he asks insultingly if any one thinks that the A on his forehead stands for France. Cheese-Eating Surrender Monkeys is a modern stereotype and during WWII, Cap actually fought beside dozens of French resistance fighters who regularly gave their lives to complete a mission or save Cap. The actual Captain America proved this point only a few issues later, during Civil War, when he makes a rather more intelligent and eloquent speech about the bravery of the men and women he fought besides in occupied France. In Ultimate Avengers, Cap was in custody of some French soldiers, who just happened to be mentioning how brave the French Resistance was. About a page later, Cap's free and kicking ass... whilst the soldiers are cringing, giving up without a fight. That's Mark Millar for you.note He licks goats, after all.
A kind of unintentional double subversion occurred in Ultimates 3. Cap's understandable shock and disgust at learning Quicksilver and Scarlet Witch are in an incestuous relationship is laughed off by Wasp as an example of his old-fashioned Puritanism. For readers however, Wasp's (and by extension the whole team's) casual acceptance of incest is extreme Values Dissonance, while Cap comes across as the Only Sane Man.
Nextwave Cap: Close your eyes, go back to Avengers Mansion, and make my dinner.
'60s-era Cap featured many similar views played straight, with Cap nudging his career-woman girlfriend Sharon Carter to resign from SHIELD so that she could be his wife; back then, that was pretty normal. Nowadays, it makes Steve look like a dick. As such, Steve is now far more progressive with his views (including bowing leadership to Wasp and serving alongside many female Avengers without questioning their abilities), and his relationship with Sharon is modernized into a Battle Couple with Sharon being the one who proposes to Steve.
The entire early run of Cap's stories from WWII fit this category, most especially the ones featuring villainous "Japs."
Similarly, in the '50s there was a run where Captain America and Bucky came back and fully embraced the idea of the Red Scare. This was later retconned to be a replacement Captain America and Bucky who went a bit paranoid after getting a bad batch of the Super-Soldier Serum.
Ultimately, the differences between original Captain America and "Ultimate" Captain America are a values dissonance between the comics industry of the 1940s and the modern day. At the time, the industry was all about big patriotism and sticking by your country in times of trouble because hey, it's your country. Nowadays, comics are more willing to stick it to the man. Thus original Cap attempted to symbolize everything best about America, while post-Silver Age Cap tries to fight everything that's the worst about it.
The Young Allies member Whitewash Jones was depicted stereotypically enough to be retconned as a stereotyped depiction of the real character in Young Allies Comics 70th Anniversary Special #1.
Early X-Men comics have some inevitable casual sexism that can be jarring to the modern reader, all the males (including Xavier) spend much of their time making crude remarks about Jean Grey and in one early issue the maid is ill so it falls to Jean to make everyone dinner (nobody questions this, least of all Jean).
Similar to the treatment of Sue Storm throughout most of the early Fantastic Four stories. Even tales that tried to demonstrate her value to the team - like "A Visit to the Fantastic Four" in FF #11 - come out painfully sexist now (as for the old running gag with Namor... let's not even go there...).
One early issue showed the team training in the Danger Room, with the male members fighting a robot while Jean - who went into combat alongside the men all the time - practiced using her telekinesis to sew.
One very early issue showed that every male member of the team was lusting after Jean, even Professor Xavier, who believes the biggest obstacle to a romance between them is his wheelchair, not that he's her teacher and twice her age. This has almost never been mentioned since then, and when it is brought up it is one of Xavier's greatest personal shames.
Sabretooth has a habit of casually referring to women as "frails." The term being slang from the 18th century -used to refer to women back when they were seen as the weaker, more frail, sex. Creed was born in the 1800s, and seems to have stuck to the name. He usually refers to many women he speaks with as "frail" or just simply "girl." Even after his Inversion, and becoming a good guy, he still does it. Rogue, Mystique, and Monet have expressed dislike of being called "frail." But Creed continues to do it, telling Rogue that if he stopped, he may as well be neutered completely. Also an example of possible racism comes up with him condescendingly referring to Silver Fox as Logan's "squaw", which could be seen as offensive now.
Similarly, Mister Sinister is an immortal from 19th century Britain and some writers, Kieron Gillen in particular, like to give him attitude and prejudices fitting that time and place - he once referred to Storm as "Cyclop's colonial pet" and when Loki called him a Frenchman, demanded an apology for a "Galic slur".
The depiction of Wolverine in Ultimate X Men has aged rather poorly since the book first saw print. While it was intended to play up his image as a bad boy and ladies' man, in a post #MeToo and Time's Up world, his sexual proclivities, which included sleeping with a barely-legal Jean Grey and trying to sleep with the very-underaged Mary Jane Watson (during a "Freaky Friday" Flip with Spider-Man, to boot, which happened because he wouldn't leave Jean alone) and Liz Allan make him come across as creepy and with the latter two, he looks like a pedophile and attempted rapist.
This idea was played with in X-Statix Presents: Dead Girl, where the Golden Age heroine Miss America was portrayed as an unapologetic racist. Ironically, she ended up in a romantic relationship with Anarchist, a black superhero she had earlier hurled a vile slur at. Miss America's racism was later used by artist Nick Dragotta as part of a justification for making the new Miss America a Latina. He pointed out the delicious irony behind making the successor of an out-of-touch bigot a woman of color.
Shapeshifting Xavin, a skrull who was the romantic partner of Karolina, was a product of Marvel's reluctance (at the time) to put openly gay characters in a series that they had hoped to market towards teenagers, which is also why Xavin's first appearance created a pretense for the newly-outed Karolina being put on a spaceship, and why, after Xavin and Karolina returned, Xavin kept assuming a male form. If Marvel had tried imposing such rules in modern times, they'd probably be subject to the kind of public-relations nightmare that DC faced when it vetoed Batwoman's lesbian marriage in 2013.
Some of the behavior of other Runaways towards Xavin would be less acceptable just nearly ten years later, after the knowledge of what behavior should be considered transphobic became more widespread.
Spider-Man: In The Amazing Spider-Man (Lee & Ditko) #8, A teacher responds to Flash's bullying of Peter by forcing Peter to challenge Flash to a boxing match. It's been decades since it would be considered even remotely acceptable for a teacher to respond to school bullying in a similar manner. Also, portraying everyone accepting a Jerk Jock as being popular has similarly become more problematic: the "wimpy" but kind and helpful Peter would be the one depicted with more friends in most modern works.
In Marvel Comics, many of the older heroes were seen chomping on cigarettes or cigars. Wolverine, the Thing, Nick Fury, heck, we see Professor X using a pipe in the first issue of X-Men! Smoking in Marvel's comics has sharply declined over the decades the same way it has in real life due to the increasing awareness of its health risks and decreasing social acceptability. Joe Quesada formally banned it when he became editor in chief due to having lost a family member to lung cancer, but it was already nearly gone by that point anyway.
Alpha Flight: The "Wanda Langowski" storyline is complicated, but in a nutshell, team member Sasquatch aka Walter Langowski is (temporarily) killed, but returns to the living when his spirit occupies the body of his then-dead teammate Snowbird; the magicks involved altered her body so that it was neither Walter's nor Snowbird's, but a statuesque 30-something woman. Walter makes one attempt at getting his male body back by visiting the mutant Scrambler who could alter human flesh, but his supernatural body wasn't affected by Scrambler's powers. Walter takes the name "Wanda" and resigns himself to living as a woman for the time being. The storyline was written in the 80s before mainstream society had any real understanding of transgender issues. Had it come out more recently, Walter would've more fully explored his options for presenting as a man in his new body if medical transition wasn't possible—cutting his hair, binding his breasts, etc.—rather than just going "Welp, I guess I'm a woman now."note Walter did eventually get his male body back, which is also a long story.
One of Iron Man's first stories features an Asian villain who has blindingly yellow skin, exaggerated features, and very stereotypical speech patterns. His skin color was not fixed for a 2019 reprint, making it even more jarring to modern eyes.
In yet another Ultimate Marvel example, Iron Man's tenancy to flirt with his female employees was glorified as part of his "ladies man" persona — and has likewise aged poorly thanks to #MeToo and Time's Up, with it now seen by many as red flags about his behavior.
Several of the old "irredeemable" Marvel villains have been given more sympathetic portrayals and motivations over the years, in part because their older stories have aged poorly. For example the female villain Nekra/ Nekra Sinclair had powers which relied on her own single-minded hatred, and she was given little to no sympathy. But her backstory is that she was an albino girl ostracized during her childhood, she was a teenage runaway at age 14, she was eventually abandoned by her best friend and lover Mandrill/Jerome Beechman, and she has been repeatedly betrayed and abused by her on-and-off boyfriend Grim Reaper/Eric Williams. Ouch. In recent years, Nekra is depicted as having deep emotional needs for love and friendship, and she is partly treated as a victim instead of an outright villain.
Similar to Black Panther's treatment up above, the early Guardians of the Galaxy stories have a lot of casual and not-so-casual racism thrown Yondu's way, with him frequently being called "savage" or "primitive" by characters and narration alike, including one point where it explicitly states his mind is "too primitive" to understand sarcasm. Now bear in mind Yondu is depicted as a Space Native American.
" in FF #11 - come out painfully sexist now (as for the old running gag with Namor... let's not even go there...).