The long-running and critically acclaimed manga by Hirohiko Araki, Jojo's Bizarre Adventure is often plagued by titular bizarre story-telling that isn't always to the benefit of the narrative. Because of Araki's strange manner of writing dialogue, and the way in which he enjoys playing fast and loose with his own established rules, many fans tend to joke about a tendency for Araki to 'forget' highly important plot points.
These jokes are also often centered around the sixth part of the series Stone Ocean. Perhaps this is due to misunderstandings, or mistranslation, but many of the complaints leveled against Stone Ocean are in hindsight easily debunked. Here are a few examples.
10 Jolyne Can Fight Stands
One of the very first rules about stand combat, established years before in Stardust Crusaders, is that humans can't even touch stands other than their own. So it came as a shock to many fans that Jolyne was able to easily kick C-Moon, and fight one on one with other enemies she encountered over her journey. The likely explanation to this is that Jolyne's stand Stone Free is made of her own body. This means that much like her friend and ally F.F. Jolyne's body and stand are one and the same, giving her the ability to physically affect stands.
9 Anasui Changes Gender
During his very first appearance, fan-favorite Narciso Anasui appears much more feminine than he does in later chapters. While popular speculation implies this was due to some dispute between Araki and his editor, this is all just rumor. What many fans forget, is that Anasui's stand Diver Down can alter bone structure. It's not too much of a stretch of the imagination to figure out that he used his stand's versatile powers to make him appear as a woman so he could move undetected through the women's prison where Jolyne was being held and where his first appearance occurred.
8 Ermes Vanishes
Jolyne's first and closest friend Ermes Costello mysteriously vanishes from the story after she defeats her nemesis Sports Maxx... Or at least that's what a number of fans seem to think.
This is by far the most easily claim of forgetfulness to debunk as at the end of chapter 57 it is stated that Ermes sustained heavy injuries in the fight and that despite the best efforts of F.F.'s healing powers, Ermes was stuck in critical care. Following the timeline, Ermes only returns after several weeks have passed and she presumably recovers from her near-lethal battle.
7 Diver Down's Power
A point of much frustration for fans comes from a lack of understanding of the stand Diver Down and plenty of fans out there consider it to be one of the weakest stands because of this. While some say, that Diver Down's power changed, others say that Diver Down has no power at all because all stands can phase through objects, neither is true. Diver Down doesn't simply phase into objects, its power allows it to restructure the object from inside as well as absorbing attacks made against whatever it is currently hiding inside.
6 Stands Can't Raise The Dead
Many people like to joke about a declaration made by Jotaro Kujo near the beginning of Part 4 of the series, that no stand can bring back the dead. While this has remained technically true, there are a few stands that push this definition like Giorno's Gold Experience. One stand that does not stretch this proclamation however is Limp Bizkit. Limp Bizkit does not have anything to do with bringing back the dead, instead, its power creates invisible duplicates of nearby dead things. Even more, these duplicates are nearly mindless and violent, a far cry from what Jotaro was explaining to be impossible.
5 Heavy Weather Makes No Sense
Weather Report and his stand of the same name are enigmatic characters throughout much of the series, but upon regaining his memories he becomes even more confusing when unleashing his ultimate power Heavy Weather (which seemingly transforms people into snails and has nothing to do with his previous weather manipulating powers).
It is explained, however, that he is actually manipulating water in the ozone to refract light and subliminally influence the people around him. While subliminal messages can't really turn you into a snail, there is science to prove they can affect the human body and Jojo has always been a fantastical series so pushing that to it's extreme shouldn't be hard to imagine.
4 Dio Suddenly Changed
Many fans remember Dio Brando as the manic and malicious villain of Part 1 of the series, or as the sinister threat behind Part 3. This image of Dio is so ingrained that fans were shocked to see a much more sensitive and calm version of Dio appearing in Stone Ocean flashbacks. However, we've only ever seen Dio when he is surrounded by enemies or minions, Pucci's memories are the first time we've gotten a look at how Dio acts around a friend and ally. This change simply serves to illustrate that Dio's feelings for Pucci were genuine rather than his usual manipulations.
3 Giorno Is Missing
When fused with the Green Baby, Pucci gains Dio and Jonathan's DNA as part of his plan to recreate the universe. As a side effect, he draws three of Dio's children to him to serve as minions. This confused many readers as former protagonist Giorno Giovanna was also one of Dio's children but makes no appearance. Comparing the four children however gives us our answer, it's simply a matter of willpower. Ungalo, Rikiel, and Donatello are easily manipulated by Pucci. The cunning and intelligent Giorno would easily be able to resist the Green Baby's lure.
2 Another Alternate Universe
With Stone Ocean's ending, Pucci is defeated but his plan partially succeeds. While he doesn't make the universe he wanted, he does restart the universe and the next part of the series also takes place in an alternate universe. Many fans seem to think these are the same worlds but there's never been any indication that this is the case.
The Steel Ball Run universe is completely separate from previous continuity, and the family tree spotted in Jojolion even proves it by showing us that the Higashikata family we see there, are not tied to the Joestars from the end of Part 6.
1 Emporio's Bone
Perhaps one of the most mysterious encounters in the series is Emporio and Jolyne's first meeting. Before Jolyne meets her father, she is stopped by Emporio who warns her away from the visiting room and gives her a malformed human bone before vanishing. A lot of fans speculate this was something to do with Emporio later traveling through time in Pucci's new universe but there's a much simpler explanation that Emporio himself gives. The bone is all that's left of his mother who was melted by Whitesnake's acid. Emporio knew that Whitesnake was waiting to ambush Jolyne and Jotaro in the visiting room and hoped that the bone would serve as an omen to ward her off.