Mostly ones pertaining to the dub:
Amara and Michelle were never cousins, it was just an honorary “we grew up together” thing.
With how hamfisted that particular plot point was shoehorned in, I think plenty of fans who knew nothing of an "original" version might have come to the same conclusion. After all, we never see any of their parents, and furthermore, there was a lack of a contrast with Serena and Rini, who were supposed to be "cousins" according to the world.
Kaori Knight and Euguel were sisters.
I can do one better. From what I gathered from
Hitoshi Doi's page and due to not seeing much art of either character...I actually thought they were the
same character because they both had red hair. I assumed that "Eudial" was Kaolinite's identity she took on after being defeated.
Then again, I also thought "Black Lady" was actually Rini's
sister when I first saw the image of her on that site (since
the original site did not have the mini-bio) and that "Prince Demando" was the father of both, so that those visions of the future were part of a predestination paradox so Serena and Darien would not be together.
Sailor Pluto appeared so small in “Secret of the luna sphere” because Pluto is the smallest planet (yes I literally thought this when we first saw Pluto when I was 7 in the lost episodes)
In all fairness, that entire episode was weird, even with full context. I wouldn't blame anyone for thinking crazy things because that was a non-standard episode even with the MOTD format.
There's actually a
very recent example that comes from the franchise's DECADES of shoddy translation work. I was actually very fond of the idea of Queen Serenity abandoning her destroyed home world and taking over the Moon, but alas, the small bit of textual evidence was debunked.
The funny thing is that this is a very popular headcanon that I've seen even well drawn doujinishi build upon.
Conversely, I'm glad this was debunked, because I loved the idea of there being an established royal line, with Queen Serenity having parents of her own, and those parents having parents. However, I then discarded the idea of a lunar royalty that extended for multiple generations because I thought it was non-canonical. Given that I've had so many ideas that were ripped to sheds, though, I can sympathize.
Anyway, I'm taking my turn, I'll be using old dub terms because that is when I held a lot of these assumptions:
The Sailor Scouts were created by the Moon Kingdom's royalty to act as planetary defenders during the Silver Millennium. I always saw the Sailor Scout as being tied directly to the ancient monarchy, not as people or beings separate or independent of it. Because I did look ahead once the dub was no longer aired, I assumed that there were "seeds of power" that the girls had, but unlike star seeds it wasn't intrinsically tied to either their life force or their reincarnation. Instead, I gathered that a group of mystics went around and looked for a young woman of each planet who was compatible with the seed and gave it to her, allowing her to become a Sailor. When the Sailor would grow old or was just tired of fighting, the wizards would then come, take the seed away and search for another host. It was only in the generation of the fall of the Moon Kingdom that the seeds were tied with the princesses and this was considered bad, because while the princesses did have inherent power of their own, as Sailor Scouts they would have to be on the front lines to fight evil.
The Moon Kingdom and the children of Doom Tree/Tree of Life were (distant) allies in the era of the Silver Millennium. Tying in with the idea of the past repeating itself, I once had this idea that the Tree of Life and its children were actually allied with the royalty of our solar system in the past. In fact, Queen Serenity's mother was being wooed by one of Alan's precursors, and she returned his feelings, but they did not marry or have children.
Crystal Tokyo is a "superhero society." Today this trope is old hat, but I once held the idea that once Neo Queen Serenity came to power...everyone got super powers. Not extended life (they still had normal lifespans), just superpowers. Most of the populace got powers due to being reincarnations of people from the Silver Millennium...people who had supernatural abilities corresponding to their planetary symbols. Actual Earthlings got powers, too, albeit more with variety. Our Sailors were still stronger than most of the populace.
The Sailors Scouts were dropped into the families of their civilian selves at their current ages, but memories were altered to allow them to live as normal humans. I didn't hold this one for long, since "The Past Returns" cleared this up, but for a second, I thought that basically the characters were dropped from the battle on the Moon to the Earth via a spacetime portal but stripped of their memories, while fake memories were planted in their surrogate families to make them accept them.
The Sailor Scouts are human aliens who like the bad guys, change into their true alien selves when they transform. You can argue this is the case, but for the longest time, I believed the girls were actually aliens, no different than Alan or Ann except that they looked human. When they transformed, they weren't simply taking on the power and form of their previous lives, but were actually becoming their old selves. Like Star Trek aliens they would have different internal physiology, like three hearts and two livers, and possibly other inhuman attributes that weren't visible.
Wiseman sent the dreams to break Darien and Serena up. I was positive Wiseman who somehow already knew Darien's identity as Tuxedo Mask and was using his power to make Darien break up with Serena. It also explained why he simply passed along visions and didn't seem to be commanding things. While this reasoning falls apart under any amount of logic, I held this thinking.
Negative energy that the Negamoon wielded aged its users. I thought that exposing individuals to negative energy artificially sped up the aging process, which is how Rini became Wicked Lady. Consequently, most of the Negamoon Family was younger than they appeared, which was why they acted immaturely; they were kids like Rini. That flashback/dream with Sapphire, Diamond, and Wiseman seemed to confirm this.
The Silver Crystal is a crystallized soul. I theorized that the Crystal wasn't just an object that could increase the power of its wielder, but that it had a will and mind of its own, as evidenced by how the Crescen Moon Wand whacked Malachite's hand on its own. I also assumed that it was the soul of the first Queen of the Moon, which is why it could not only work magic but could specifically be wielded by the royalty of the Moon. I gathered that the Silver Crystal was the embodiment of the soul of first Queen of the Moon.
The attack of the Negamoon changed the planets from habitable worlds to their current state. I held the view that the Solar System had nine habitable planets, and somehow, it was the Negaverse's attack which reduced the planets to being inhospitable to life. Mercury, despite being close to the sun was a cold - but habitable - planet with lots of snow.
People aligned with the planets of Venus were unique in that they could revert to being of the Moon. That is why Sailor Venus could be Sailor V with all the crescent moon trappings, because as a population, the people of Venus were similar to those of the moon and when stressed would involuntarily revert to that state.
All of the people on the moon had the crescent moon mark on their foreheads. I was so inobservant that I didn't even notice that Queen Serenity's crescent moon symbol was jewelry and not an actual crescent moon mark, I assumed everyone who was affiliated specifically with the moon, much like the cats, had the crescent moon symbol. I did not think it was reserved for the princess.
Rini is the reincarnation of Queen Serenity. This is another one of those theories I only held
very briefly, but I did hold it. How could a bratty half-pint be the reincarnation of one of the most self-sacrificing character of the franchise? Because as Queen Serenity mentioned, perhaps they would meet again. She might have sent herself to the future, but not in the same wave. Given that the magic of the crystal/wand managed to seal Luna and Artemis in suspended animation, then it could have worked on her dying soul . Also, given that Rini did mature after her atrocious behavior in R was a sign she was her own grandmother after all. Also, given that Queen Serenity stops appearing in the old series after Rini makes her debut, I made a connection when there was none.
Greg, Game Machine Joe, and the other Rainbow Crystal carriers were going to come back. Given that they still had their talents and Greg was mentioned by the dub, I got the impression these characters were going to join the fight against the Negaverse with their power. I even assumed they would be able to utilize a hybrid battle armor between their monster forms and their human ones in order to fight against new threats. The Sailor Scouts would still save the day, but they would get help from their friends.