The manual for Interplay's PC adaptation of The Fellowship of the Ring had a section explaining that the portrayal of some elements of the setting reflected the source material and might conflict with modern sensibilities.
Natsume has run into this a few times in translating the Harvest Moon games.
The Japanese Harvest Moon DS Cute had a Romantic Two-Girl Friendship / Gay Option, where your girl could engage in a "Best Friends Ceremony" with some of the other female characters, at which point they'd become essentially the same as a wife. Although relatively mundane for Japan, this would be considered shocking to certain parties in the US, so was quietly dropped from the US version of the game. Both dropping it and the way Natsume handled dropping it have upset fans, though.
There was also Harvest Moon GBC 3, which gave a choice of playing as either a male or female. The male character could get married and have a child and continue playing. The female character's game ended as soon as she married. Also, the love interest for the male character was completely useless until livestock was purchased, which could only be bought after growing a certain amount of grass. The love interest for the female character merely began as incompetent.
In Back to Nature For Girl, your game also ended after you became married. Though this was changed in the enhanced port-remake, More Friends of Mineral Town.
If it's historical and has a level of detail beyond personally killing things (effectively, a strategy game), it probably qualifies. Take Rome: Total War: the men in your family line are the most important characters in the game, providing bonuses when they lead armies and run your cities, with stats and intricate trait and retinue systems; the women don't even have stats, they're used for making babies and bringing new men into their family.
Slavery is a particular problem with historical building games. Some use it as a critical game mechanic, others pretend that it didn't happen. In Medieval: Total War, if one is playing as a Muslim faction, it is possible to sell captured soldiers/rebels into slavery (for Christian factions, the option is "execute"). It is also possible to launch Crusades or Jihads against another group.
Each province in Europa Universalis III produces a particular trade good. In Africa, one of the possible trade goods are slaves. The game, however, gives the player no benefit for finding slaves other than the actual direct profit from the trade good... and even then, one prefers to find gold or ivory (Another resource that conjures values dissonance) in Africa. It's possible to abolish the slave trade, at which point all of a player's provinces that "produce" slaves start producing something else; this is usually beneficial, because it gives players another shot at finding gold in their provinces.
Whether you want slaves or not actually depends on economic reasons, just like in actual history. Slave producing provinces give a big bonus to provinces that produce cotton, tobacco, or sugar; and if you abolish the slave trade, you're just as likely to find near-useless millet as you are ivory or gold. Even if you do find ivory or gold, it isn't a huge step up from slaves; and if you own more than a few of the aforementioned provinces that benefit from slaves, you're likely to lose money even if you strike nothing but gold.
Victoria an Empire Under The Sun and its sequel have gotten a lot of flak over the use of the terms "civilized" and "uncivilized." All the countries in the world are divided into these two categories, with "civilized" countries being able to industrialize much easier and research technology much better. This rather simplistic dichotomy works well for game balance purposes, but still generates controversy. The developers respond that the game, which covers the period of neo-imperialism and the heyday of scientific racism, is by its very scope Eurocentric, and that their detractors are just reacting badly to values dissonance.
Hideo Kojima's self-confessed fetish for demure, quietly emotional women was never so bad as in Snatcher, where the thirty-two year-old protagonist has a sexually-charged fling with a demure, quietly emotional fourteen-year-old model. (To give you an idea of the sexualisation, she has a birthmark on her inner thigh shaped like a heart, and you actually need to know that in order to continue the game. You can also make the protagonist sniff her panties and, at one point, he sneaks up on her naked in the shower.) While side characters complain, it's because the man is technically married, although no side characters comment when another female character asks him out and he accepts. The localisation aged her up to eighteen and removed the panty-sniffing and nudity.
Something similar happened in Metal Gear Solid. It's worth remembering that the plot involves an eighteen-year-old who has never had a previous relationship hooking up with a thirty-two-year-old, and that no-one at all thinks this is odd -- in fact, the other characters actively encourage it and point to her youth as a reason why she's perfect for him. It gets worse when you remember that Meryl was originally going to be thirteen (modelled after Natalie Portman's character in Leon/The Professional), and was only aged up to an adult because the character designer had trouble imagining a thirteen-year-old handling a Desert Eagle like in the script.
This is itself an example of Values Dissonance -- 16 is the Age of Consent in most of the developed world, including most states in the US. People in the US tend to think of treating 16-year-olds as sexually available adults creepy because 18 is the age of consent in California, which produces much of the US's entertainment and exports its ideas about the appropriate age of consent and when someone can be considered a mature adult to the rest of the country.
This is also slightly mitigated by the fact that Paz is not actually 16 years old.
The European version of Platinum removed the slot machines because PEGI has gotten harsher on gambling references. Moral Guardians elsewhere complained too, and starting with HeartGold and SoulSilver, the slot machines have been removed from the international release of future Pokémon games.
The Disgaea series is consistently rated A in Japan, the equivalent of E or a low-end E10+, and is marketed accordingly. In America, the games are rated T and aimed at teenagers and adults, as the games have a lot of Fan Service designs and shots, particularly after a battle is completed. The English translations also tend to have a moderate amount of profanity.
Shirou Emiya of Fate/stay night earned a large amount of fan hatred for his seeming Stay in the Kitchen attitude towards Saber's fighting in the Grail War. In fact, he's actually a subversion; he's just mortally afraid of Saber dying (and painfully aware that he's not qualified to fight alone) and initially doesn't understand why, settling on a traditionalist view as a random excuse. Notably, he doesn't act this way towards any other woman (even Saber herself in the non-Fate routes), and the very idea is even mocked on occasion.
This doesn't dismiss his approval of Ayako's attempted rape for 'teaching her femininity'. However, this along with Stay in the Kitchen, fades from the later arcs.
Um, what about Mara? Its presence alone should be enough to force an M rating on any Mega Ten game it's in.
The makers of Shenmue II are guilty of this by having a barmaid, in the BRITISH Colony of Hong-Kong; thank Ryo for being so honest about being too young to drink buy alcohol at age 18.
Sort of noticeable in the Metroid series of games: in the Japanese-made 2D games, Samus is a somewhat understated character, implied to not be terribly well-known outside of people who need to know who she is (typically, the Federation and some of the Pirates that she has history with). In the American-made 3D games, Samus is well-known by nearly everyone, played up like some sort of celebrity or war goddess, universally feared by the Pirates and well-respected by even the newest recruits in the Federation; in other words, a more Hollywood-esque portrayal of a heroine of her stature. Incidentally, the Japanese 2D games are also the ones to show Samus scantily clad in her "reveal", even as recently as Zero Mission, the first 2D game to show her in her Zero Suit (which appear in some of the endings, but she's wearing less in others). It was the Americans who first made an attempt to cover her up, with Prime never showing less than her without her helmet, and Prime 2 introducing her slinky but functional-looking Zero Suit.
Of course, this has led to a large quantity of Americans Hate Tingle with the latest release in the series Metroid: Other M; some of which being the various materials that were published to establish her emotions. For instance, the Japanese viewing "Bounty Hunter" as just a cool title rather than a badass anti-hero and/or amoral law enforcer, with a proposal in Prime 3 by Retro for side quest bounties being denied by Nintendo as something a good person like Samus would never do.
In the Japanese release of Earthbound (Mother 2), in the Town of Magicant, which exists only in Ness's mind, the protagonist is naked (a Japanese symbol of purity), while in the US he appears in his pajamas.
While received favorably outside of Japan and generally seen as a fun and heartwarming game with tons of Video Game Caring Potential, Valkyria Chronicles has a strongly Japanese ideal of unity and has a tendency to kill anyone with a unique character design who either doesn't wear some type of uniform, or betrays the one they have. It leads to some Family Unfriendly Aesops when it comes to the titular Valkyria, who disavows her superpowers essentially because they make her stand out too much.
That... might explain why Valkyria Chronicles III completely went the other direction when it comes to values (except Camaraderie, that's inviolable). Your characters are society's refuse, they constantly go against their superiors' orders (for better or for worse), at some point they have to fight and kill their own countrymen, and their Valkyria, Riela, is not trying to do anything to change people's perception of her as a "freak". VC 3 thrashes the usual Japanese values out of the window and then tosses live grenades on them just to make sure.
Rule of Rose was subject to this trope in many parts of Europe where the publishers were pressured to pulling it out of the shelves. All because it depicted children as something other than innocent little angels, capable of extreme cruelty and spite, and possessing early signs of developing sexuality -- even though nothing unwholesome happens with preteen children in that area, and the sexual abuse of a sixteen-year old girl is treated with all the horror it deserves.
The Nancy Drew game Shadow at Water's Edge plays with this trope, as it is set in Japan. Part of Miwako's resentment towards Yumi, apart from sibling rivalry, is that she left the Ryokan to start her own career making bento instead of staying to run the hotel as expected of her. According to Miwako, this makes Yumi "selfish". This logic only makes sense if you understand that in Japan, independence is frowned on and that you're supposed to do what's expected of you. However, it is also revealed later on that the girls' mother actually wanted them to lead their own lives and not take care of the Ryokan unless they wanted to do it, proving that the general attitude towards an issue does not necessarily hold up for everyone.
Godot, a character in the third Ace Attorney game, is viewed by western audiences as sexist and patronizing towards women: he refuses to take Franziska seriously and tends to refer to her by condescending pet names, not to mention his insistence that Mia needed to be protected, if not by him then by Phoenix. While it is still presented as a character flaw in the Japanese version, it's not presented as serious a flaw; as a result, he's pretty much universally beloved in Japan.
Japan insisted on partial removal of nukes from Fallout 3 before it would permit release in the country. Specifically, the nuclear bomb in Megaton could originally be either permanently defused (good option) or rigged to blow up the entire settlement (evil). The Japanese version removes the latter option and also renames the "Fat Man" nuclear grenade catapult to "Nuka launcher". Strangely enough, the weight-reducing modification kit for the weapon apparently retained the name "Little Boy".
An interesting in-story example occurs in Mass Effect 2: The asari regard their Justicars as great heroes, with almost no one seeing any objection to their license to kill anyone they regard as an obstacle at solving crimes and their code of honor that places them outside the law. However, even asari police officers understand very well that having a Justicar interacting with non-asari guarantees diplomatic nightmares. To anyone who is not very familiar with asari values and customs, Justicars are psychoticBlood Knights who will murder everyone with a face they don't like.
This trope is part of the reason American Kirby Is Hardcore exists. While video games make cute characters and box art a common selling point in Japan, in America it is relatively a niche market outside children or casual gamers. Attempts to move towards the happy box art of most Japanese games is far outweighed by the amount of box art that turns them into sword-wielding warriors or have them wear scowls on par with Jean-Claude Van Damme. Case in point-the Starfy series was a big hit in its native Japan, but despite a fun and unique gameplay style; the cutesy appearance of the title character caused the series to be a commercial failure in America and localization attempts ceased after a single entry.
Quite a few games with an ESRB rating back in the 90s when released today have had a change. For instance, a few K-A (Ages 6+) games get slapped with the newer E10+ (Ages 10+) or even T (ages 13+). The new ratings come with extensive lists of possibly objectionable content listed on the website as well, which allows consumers to make a more informed decision based on their own values and avert this trope.
The opposite happens, too: In 1984, Germany banned River Raid for its violent content; in 2002, the ban was lifted, and it was rated free for all ages.