A lot of reviewers of Kanon complained that the scene in which a character gets hit by a runaway car looks unrealistic, since the victim cannot be seen anymore. In reality that is likely to happen when the car actually covers the victim or when the victim gets catapulted out of sight, as can be seen on footage of real accidents. And, after that episode was aired, people found footage of an accident on YouTube which was identical to that scene. It's quite possible that it was the one used by the animation team as a reference.
One criticism often leveled against is that its characters are unrealistic. The depiction of their dysfunction is supposedly too extreme to be believable. In fact, the main trio's personalities match up very well to genuine mental problems, to the point where it seems probable that they were consciously modeled after them. The in-universe explanation for why all the Eva pilots happen to have deep-seated emotional problems is All There in the Manual.
A number of commentators, including this reviewer, have noted a lapse of realism in Tokyo Magnitude 8.0 — a conspicuous absence of rioting and panic in the wake of the disaster. Ironically, the 2011 Sendai earthquake revealed that this was in fact a perfect representation of Japanese cultural sensibilities. The reaction of the Japanese people was indeed extraordinarily level-headed.
It should be noted that many Western media reported the more or less total lack of looting in Kobe, following the Great Hanshin earthquake of 1995, with considerable undertones of awe. Add to this that the Japanese are widely considered as a society striving for consensus and collective good and this turns into a major case of the reviewer not doing his research. Not to mention, lying on the Pacific "Ring of Fire", they're kinda used to these things. It was a different case with the Kanto Earthquake in the early 1900s where riots did go out of control.
Yasuna from Kashimashi: Girl Meets Girl has a physical condition where she can't see men's faces. It comes off as a blur in the anime, and an outline in the manga. A lot of fans and critics believe it to be an outlandish made-up disease or a psychological problem. Her condition is actually very similar to a real disorder called Prosopagnosia, albeit hers is probably a mild form... In the manga at least. One sufferer of the disorder has stated that the portrayal is rather realistic. The anime version makes clear that it is a psychological problem, though, considering what happens by the end. The climax of the anime and manga are very different.
Used in a very 'meta' manner in Cat Planet Cuties. Eris - a bona-fide Cat Girl alien - gets targeted by a Secret Society of hardcore sci-fi fans who simply refuse to accept that humanity's First Contact is with a Human Alien - they want something PROPERLY alien! Even better, Kio brings Eris along to help his movie-club shoot a sci-fi movie, but not only is Eris not alien enough, her Assistaroids look fake, and - here's the kicker - her spaceship, which she can remote-control, uses a form of superstring braking to maintain flight at very slow speeds, which resembles... strings, going upwards from the corners of the ship. So her ship ends up looking ridiculously fake in all their shots as well. Ultimately, they decide to scrap the sci-fi plot and shoot a Romantic Comedy instead.
When people want to paint the Leo from Gundam Wing as a shoddy piece of junk, they tend to cite scenes in which merely being near the blast from Wing's rifle is enough to destroy one. This is, however, a rare aversion of Convection Schmonvection in the Gundam metaseries, as a gigantic wave of super-charged plasma would generate some pretty intense heat.
The same effect is shown in Gundam Unicorn, in which a mobile suit is blown up when a discharge from the Beam Magnum passes near it. The other pilots take this as an indication of the beam's extreme power.
In fact, as far back as the original Gundam novel trilogy written by Yoshiyuki Tomino has this been used. In fact, there's a scene where Char Aznable tells other soldiers that if you see the barrel of a beam cannon, you're dead.
Not involving any sci-fi elements, in Mobile Suit Gundam SEED Destiny, Shinn keeps around his dead sister's cell phone and listens to her voicemail message when he's down. Now, it's fairly common behavior for people to keep answering machines and old family movies with people that have died. With the Fan Dumb however, they view Shinn as having something wrong with his head because of this.
Some viewers of Sound of the Sky complained about how ludicrous the old house perched on a cliff shown in the first episode was. The whole series location is an accurate recreation of the Spanish town of Cuenca, and the house is a popular tourist spot.
May, Dawn, and to a certain extent Misty (even though the last one is actually flat-chested, something explicitly stated on the show) are often accused of being unrealistically "well-developed" for a 10-year-old. In reality, puberty for young girls has gotten much lower in recent generations because girls are fatter than they used to be (a girl needs a certain amount of body fat before she can begin puberty). Thus the average age for puberty to start in girls is actually at nine and ten years old. Not surprisingly, this shocks people in real life as well.
On a completely different tangent is Brock's ethnicity. Most Americans think that he is Latino or Black or so on. Turns out that it's really not that uncommon for Asian people to get that dark. Ash himself is also fairly tanned. This, despite that a minor celebrity in the U.S. is Julie Chen, a former newsanchor, host of Big Brother and a talk-show host in the off-season.
Fans legitimately complain about the ridiculousness of characters surviving unsurvivable injuries. The oft-ignored in-universe reason is that a character's vitality levels affects their survivability, and the reader doesn't see the Life Meter. However, the main example used is Hiyori being cut in half. Instead of instantly dying, she survives long enough to receive medical attention which saves her life. Ignoring magic unrealistically reattaching her body together, real life humans genuinely can survive being cut in half as long as medical intervention occurs quickly enough.
Some American fans complain that it's unrealistic, even accounting for Japanese cultural privacy, for fifteen-year olds to live alone without any legal guardians or state intervention. However, in Western countries, including America, teenagers who are legally minors can indeed be found living alone without any guardians or state intervention. Psychology research has identified many reasons, including: parental abandonment/neglectnote (Mizuiro's mother isn't raising him, so he seduces older women to play a parental substitute role in her stead), death of any/all guardiansnote (Sado's parents died when he was eight and his grandfather died before he reached fifteen), parental abusenote (Three-year old Orihime was kidnapped by her eighteen-year old brother Sora to save her life from parental abuse. He died nine years later, leaving Orihime alone), walking out on the parentsnote (Uryuu walked out on his father in disgust when he realised Ryuuken hates being a quincy, although it's strongly implied Ryuuken quit being quincy to save Uryuu's life, and is still secretly protecting him), or arrangements with family that allows for the child to be independent of all direct intervention except for financial supportnote (Orihime's independence is actually funded by an aunt who has nothing to do with Orihime on a daily basis but who funds her on the understanding that she does well in school, which she does). In short, all the manga examples do occur in real life, even in the US.
Wandering Son fans bemoan that Takatsuki no longer considers themselves transgender by the end. People cry that it's unrealistic and OOC, but studies have shown that many children who can be considered transgender grow up to be cisgender identified when they're older. Also, it's left ambiguous in the end whether they're really cis or it's a phase due to confusion, having no support, and lack of confidence. Takatsuki did have a lot of foreshadowing prior to the conclusion.
A complaint some people have with Michiko & Hatchin is that it takes place in a fictional country heavily based on Brazil yet almost everyone has a Japanese given name even when they don't seem to be multiracial. Ignoring the fact it's a fictional country and thus it could have a history with Japan, Brazil itself has a rather large Japanese population. Brazil also has a very high miscegenation rate, meaning that it's entirely possible to run into people who look black or European, but still have Japanese names.
Tsuki ga Kirei has a relatively realistic depiction of first love between two teenagers developing over time. However many viewers faulted this series for having development that was too slow and chaste because of they had grown accustomed to more energetic and comedic romance anime. The ironic thing is that studio feel had itself contributed to this situation through the shows they worked on in the past.
Due to the fact that many anime and light novels exaggeratedly show ordinary people as impenetrable idealists and born heroic personalities, especially ordinary school students, Subaru from Re:Zero may seem very repulsive and stupid because his image is as close as possible to the idea that as if a real ordinary teenager acted in such a situation and through which he would have to pass before becoming strong.
One of the complaints fans had with Sailor Moon Crystal was towards the Guardians' designs looking much older than their actual ages, having long proportions and thin frames as well as more traditional shoujo-esque eye designs. As a result, there were those asking for a redesign to make them more in line with the "real" designs of the 90s anime. Problem is, the redesigns were based on Naoko Takeuchi's original illustrations for the Nakayoshi serialization, right down to the older, thinner look (Takeuchi based the style off of fashion illustrations). Thanks to good ol' Adaptation Displacement and marketing of the anime lasting years, the character designs of the first Sailor Moon anime became so iconic that the original look seems less real and more "stereotypically shoujo". Fans were more receptive to their redesign in season 3, where they managed to meet in the middle for the poppy, proportional 90s and leggy, model-esque manga aesthetics.
Date A Live has an in-universe example in the dating sim that Shidou is made to play. He calls the situations portrayed in the game (such as a Little Sister Heroine dancing on top of the player character, giving a Panty Shot) unrealistic, except that they either have happened to him recently or happen soon after (to use the same example, his actual little sister really did that to him).
Fullmetal Alchemist: Winry and Riza's names are often mocked for being "nonsensical". This has led to the urban legend that their names were intended to be "Wendy" and "Eliza/Liza/Lisa" but weren't translated correctly. However, both their names are real names, albeit "Riza" is more commonly written as "Reza".