Adaptation Induced Plot Hole / Sailor Moon

• At the end of the first act of the manga, Innocent Bystander Naru is insistent that morning that she and her mother were attacked by "robbers" the previous night (which fits somewhat with the fact that her mother was found taped up and locked in the basement of her jewelry store), who were stopped by Magical Girl Warrior Sailor Moon (she has mercifully forgotten they were a shapeshifting monster). In first episode of The '90s anime, rather than operating under a Weirdness Censor, Naru believes the full incident was All Just a Dream, which raises questions as to whether she remembers that the "dream" monster told her that her mother was Bound and Gagged in the basement.
• In the Sailor Moon S season, the then-currently condescending Outer Guardians have an oddly polite conversation with Tuxedo Mask (despite him being one of the weakest Guardians) and refer to him respectfully as Endymion, despite no other indications that they know much about the existing cast (barring Pluto). This was lifted almost directly from the manga, where the Outer Guardians are implied to already know who most of the Guardians are/were but are avoiding working with them out of a sense of duty and penance rather than dislike and skepticism.
• The anime never explains how Mamoru is able to keep Chibi-Usa alive at the end of Sailor Moon S when her heart crystal is stolen. This is a plot point that is lifted directly from the manga, but by this point the story had already established that he has the power to pass on energy to another person and even heal wounds several times. The anime never establishes him as possessing such a power, but it acts as though he's been able to do this all along.
• The anime short film Ami's First Love (accompanying the Super S movie) is a straight up adaptation of one of the Exam Battle short stories in the manga, which is about Ami getting a love letter from a secret admirer and freaking out so much she breaks out into hives. The problem? In the anime's timeline, Ami has already had a brief relationship with a Canon Foreigner fellow student, Urawa Ryou (thus this isn't even her first love) and she was shown handling his shy affection for her with grace and maturity. The short film also has the problem of showing Ami using an attack that she only used in the manga without explanation of where she got it. The films already create so many continuity problems that they're generally considered non-canon anyway, but it's still jarring when a story from the manga is adapted straight into a timeline that proceeded so differently as to contradict it.
• A minor issue is with Uranus being mistaken as a boy. In the original manga, she is intentionally disguising herself as a male student to investigate the Mugen academy. She even poses as a new Tuxedo Kamen in one scene. Sailor Moon only realizes that she is a girl by recognizing her as Sailor Uranus. In the anime, she is simply a tomboy. It never gets explained exactly why Minako and Usagi initially mistake her as a boy, or even why Minako realizes that she is a girl in the end.
  • The same episode where the girls mistake Uranus as a boy also has Neptune deny that they are a couple, even though it was just as obvious.
• A minor plot hole happens in SuperS in regards to the Amazons Quartet. At the very end of the series, they make a comment about possibly meeting Chibimoon again, and it is also never explained why they're named after goddesses/celestial bodies (a Theme Naming pattern common for the Solar System Sailor Guardians) rather than minerals or metals (a Theme Naming pattern common for the antagonists) — the implication is that they used to live in the asteroid belt, which only raises questions as to their true origins. In the manga, the four of them were actually dormant Sailor Guardians meant to be Chibimoon's guardians, who were forcibly awakened before their time and brainwashed into working for Nehellenia; their names come from the four asteroids that grant them their powers. Because the anime deviated from the manga in handling these characters, and ended up having Chibimoon herself Put on a Bus following the first arc of Stars, this development never happened in this version, leaving the hints that there was more to the Quartet with no outcome.
• In the Sailor StarS season, many characters remark that Chibi Chibi looks exactly like Usagi. Not just like her little sister, more like her daughter. Well, in the manga, this did make sense as Chibi Chibi is actually Sailor Cosmos, a future form of Sailor Moon herself, and thus they are essentially the same person. In the anime, however, her origin is completely independent of Sailor Moon entirely and it's never explained why they look similar.
• In episode six of Sailor Moon Crystal Usagi freaks out that she can't transform in front of Tuxedo Mask and reveal she's Sailor Moon, a few minutes after telling him she feels powerless as a leader. She's then surprised to learn he already knows about her secret identity. In the manga, he tells her he knows before she starts worrying about her inadequacies as a Guardian, so her reaction makes perfect sense. (Out of context, her words could be interpreted in a more general sense since she doesn't specifically mention the Sailor Guardians but talking about having to protect everyone while there's clearly a fight going on not too far away doesn't leave much room for interpretation.)
  • Near the end of the same episode, Tuxedo Mask carries an unconscious Sailor Moon to his home so she can rest after overusing her powers. When she subsequently wakes up in Mamoru's room, she is detransformed, with no explanation why this happened. In the manga, she detransforms at will upon waking up, and in general it is shown that simply being unconscious doesn't make a Guardian spontaneously revert to the civilian form, so it's unclear why her transformation was undone in this case.
• Another episode of Crystal recreated the scene from the manga which reveals that Mamoru survived being stabbed by Sailor Moon because the stones the Shitennou transformed into blocked the blade, preventing him from receiving a fatal wound. In the manga, the possessed Mamoru was explicitly shown carrying the Kunzite stone after the Shitennou's human bodies decayed. In Crystal, however, the Shitennou didn't die until shortly before Mamoru was stabbed, which happened in a different place, so there's no explanation why he had their stones at that moment.
• Another problem that occurs with the alterations to the Shitennou's plotline occurs when a brainwashed Mamoru brainwashes Motoki to hold off the Guardians. Any viewer who hasn't read the manga will likely be scratching their heads as to why he doesn't just use the Shitennou, who have been proven to be more than a match for the girls before.