JOJOLION PLOT POINTS
Bite marks (dropped/retconned)
During the first chapters of Jojolion, "something" bit Josuke in the neck around his star birthmark and Joshu and Yasuho in their legs without them noticing while close to the Wall Eyes. Said bites are implied to have given them their Stands. However, during Vitamin C, Josefumi is shown to have had Soft & Wet from the beginning (although the bite might have allowed Josuke to regain the Stand in that specific case since he is Josefumi "reborn"). Daiya also states in California King Bed that she fell in/near the fault lines and developed her Stand while losing her vision afterward. Josuke's bite mark was shown again in vol 18. Volume 25 shows Yasuho had her Stand as a kid. In the end, the bite marks are never acknowledged or explained.
Flashback Man (retconned)
Appeared in a mid-combat flashback with Kira during Vol 2, but in Going Underground/Born This Way Josuke states he has no memories from his previous lives.
Kira has no family (retconned) - his mom Holly is a university professor and currently a medical patient and his sister Kyo (formerly Kei) is the Higashikata Maid (retconned)- THIS PERSON DOES NOT EXIST(retconned) -THIS PERSON DOES EXIST
Kei was taking care of Holly off-screen all along except when she wasn't.
Kira died of illness (retconned), Yotsuyu was involved in Kira's death, Yotsuyu killed Josuke's non-Kira half (Kujo Josefumi)
The official cause of Kira's death according to Yasuho was illness (heart attack?). In I Am A Rock, Yotsuyu proclaims that if wasn't for Kira then Josuke's other half would've died between the rocks. In the Vitamin C flashback this is almost entirely retconned, as Kira was out of action and dying to both Damo slicing out his liver and shrapnel from his own Sheer Heart Attack in his head. Josefumi solo'd the A. Phex twins in the woods of the Higashikata property, and Yotsuyu never fought him. Josefumi technically killed himself via equivalent exchange with Kira.
Evil Norisuke (dropped + retconned)
Norisuke was definitely portrayed as ill-intentioned in the earliest volumes of Jojolion. He even threatened Yasuho (via Kei) that if she approached Josuke again her family would die. During California King Bed his internal monologue indicates he wanted Daiya to take all his memories and turn him into her slave, then kill him for fucking her. This is reiterated at the start of Going Underground/Born This Way when Norisuke is shocked by how Daiya is acting toward Josuke. By the time of Yotsuyu arc, Norisuke has been retconned into having a self-serving but not malevolent motivation of figuring out what Kira know of the "cure for rock disease", and he has no reaction to Yasuho being on his property (although she never is allowed back despite being "Joshu's girlfriend")
Daiya was supposed to mindbreak + enslave Josuke (dropped)
As noted above, Norisuke originally wanted Daiya to specifically steal all of Josuke's memories and turn him into a slave.
Bookseller's mark (dropped)
In Vol 2(?) Kira's corpse is shown with a "bookseller's mark" on the wrist. This same mark is on the railing leading to Norisuke's library, the only room he forbids Josuke from entering. After losing and regaining the memory of the mark, he goes upstairs and finds the "Steel Ball Run" book with the same mark, which contains the Higashikata-Joestar family trees. It is never explained how Kira got that mark or why he was investigsting the Higashikata family tree, and the flashbacks during Vitamin C do no show it.
Holly's Stand (dropped)
In Chapter 14, Holly explicitly sees Paisley Park being subconsciously used by Yasuho, which implies that she possesses a Stand herself. It should be noted too that Holly in her first appearance is pretty lucid and just "quirky," even the doctors state she's been living a normal life. The Vitamin C flashback shows her in a worse state closer to dementia, which is carried on in the aftermath of that arc.
Josuke wants to go to school (dropped)
This was the setup for Shakedown Road but was discarded in the next arc.
Johnny in Japan
The story of Johnny, Rina, George, Rock Disease, and The Corpse hasn't concretely tied into the plot yet.
weird baby that washed up on the beach after Johnny's death (rock baby?)
Kira in Higashikata Rape Dungeons near where Josuke was "born" (retconned?) - actually that was Yotsuyu's room and Tsurugi was lying to the readers? (raughs)
During Paper Moon Deception, Yasuho noticed a room in the underground passage with a sailor uniform and robots inside and commented it looked like a jail, and later Tsurugi says that "Josuke" (Kira) was in that room before. During I Am A Rock, Norisuke says that room belonged to Yotsuyu. Tsurugi also stated during Paper Moon Deception that the complex was were the family researched cures for the rock disease but there was no followup. During the Vitamin C flashback, Kira isn't shown having any sort of interaction with the Higashikata. In vol 18, Rai guides Josuke to a secret passage (that only he and Norisuke know about) for "cultivation and harvesting of special products" in the Higashikata orchards.
Firstborn Higashikata getting the rock disease
This is contradicted during Johnny's flashback after Shakedown Road where Rina, the secondborn Higashikata of Norisuke the First (the firstborn was Johei/Norisuke the Second), had the rock disease.
Tsurugi dresses like a girl to ward away the rock disease curse
Stated by him in Paper Moon Deception, contradicted by flashbacks that show both young Norisuke and Joubin clearly dressed as boys.
Holly possibly having rock disease (retconned) - Holly was constantly administered Rokakaka to shut her up
During the first arcs, Holly is said by Norisuke to share "the same fate as the Higashikata" and similarities are made between both illnesses. During the final arcs, it instead turns out the rock human doctors have been constantly administering her Rokakaka in order to get her out of the way and her "disease" gets changed from missing perfectly cut parts of her organs to rock moving up her body.
Kira had a cure for rock disease (retconned), Kira came to Morioh looking for a cure to rock disease - Kira had a Rokakaka tree (or 2) in his apartment specifically because he was trying to cure Holly (retconned) - Kira and Josefumi kinda stumbled onto the rokakaka fruit and stole it to cure Holly - Josefumi grafted a rokakaka branch to another tree and tended it
One of the most retconned plot points. Also worth noting that vol 22 retcons that Kira told the s-rfer about the rokakaka, its origin, equivalent exchange, and Holly.
ROCK HUMANS; like normal people but ROCK except they're icky 'parasites - Rock humans are a fallback in case carbon-based life fails
The rock human lore changes between its 2 big appearances in the Love Love Deluxe (Part 4) and Wonder of You (Part 16) arcs. LLD says rock humans fall in love with humans of the opposite sex on rare occasions but break up 97.5% of the time in the form of murder, that they biologically cannot have children with humans, that they transform every 6 years by molting, and that they hibernate for months so they cannot hold jobs with business hours. WoU says rock humans don't feel love or friendship (contradicted many times), that human males CAN reproduce with rock human females but not the opposite, and that they only have one huge transformation at 17 years old while leeching off wasps inside a nest. Their hibernation is not mentioned at all even though it would be important for the story of the rock human doctors and how they keep their covers (and most importantly, jobs at the hospital where their Rokakaka scheme takes place).
Jobin is connected to the rock fruit trade (which isn't illegal but that makes it even worse)
Jobin was Damo's connection to shipping and storage for the Rokakaka operation.
Tsurugi's actions are righteous (retconned)
While Yotsuyu is drowning, he claims to Josuke that Tsurugi's actions are the righteous ones as if he or the rock human group had some plan for the boy besides using him to drag Josuke out. This is contradicted during Doobie Wah! where Aishou just plain wants to kill Tsurugi after learning he was tailing him. There's no interest of the rock humans in Tsurugi at all afterwards and his actions are in clear opposition against them.
Yotsuyu built the stadium Aishou worked at and which contains THE 'fruit'
This was never followed up and subsequent volumes establish that Aishou merely store the plant there after importing from New Guinea.
Karera was Josefumi's stalker (raughs), hated Kira (despite his 'knowledge of the world' saving her), and was being watched by the ROCK MAFIA; she will return SOON
Karera recognized Josuke as Josefumi despite everyone else recognizing him as Kira. She implied she and Josefumi may have fucked at one point. She took Josuke to Josefumi's address. She showed him a picture of Kira, Josefumi (forma de Joestar), and herself. She talked about Kira, how she hated him, how he had a rokakaka tree in his apartment (and we are actually shown a panel of it!), and how his "knowledge of the world" saved her. But Vitamin C totally debunks all of that. Kira never had a tree, Josefumi just grabed some branches and grafted them. Kira and Karera didn't know each other. She was Josefumi's stalker classmate. There was never an occasion were the selfie occurred, and Karera would have had no way to know ANYTHING about the rokaka at all. During Vitamin C, Josuke was having Yasuho try to look up his address even though Karera took him there.
the wall eyes combine things that are buried, they exist to protect something, they existed before the quake (retcon)
Vol 1 states that while fault lines existed in Morioh since time immemorial, the Wall Eyes are a recent phenomenon after the earthquake. In Lemon & Tangerine, Kei/Kyo, shows the wall eyes' combination power on fruits, essentially stating that Josuke was created by Kira and another person being buried near the wall eyes. Vitamin C contradicts most of this, as the wall eyes exist and are named before the quake (although they are smaller), and Josuke's creation is attributed to the hybrid "new rokakaka" equivalent exchange effect. Damo states the wall eyes must protect something.
Josefumi's birthmark (retconned)
A controversial point, Josefumi is drawn with the Joestar birthmark multiple times during Love Love Deluxe, which was not seen in Vitamin C and edited out of later reprints of the arc. The fact that his phone has "Josephmi" on it might be an indication that Araki intended Joseph Joestar to be his father. Turns out his name is because Josefumi's grandpa found a shoe that belonged to Joseph Joestar and the name burned itself into his mind (raughs)
why do the Rock Doctors care about rokakaka?
Rai (via a long schizobabble infodump) states that the Rock Doctors want to monopolize the fruit and use it to get rich. Urban Guerilla explicitly dismisses money as a goal, implying that it is evolution of some sort that they seek.
Yasuho is going to analyze her dead rock animal hairpin; it might be a lead towards the identity of the rock humans (dropped)
After dumping her backstory, Yasuho says she's going to investigate her hairpin to find a lead on the rock humans; the next time we see her, she's in the hospital because of her period and whatever results her investigation may have had are not acknowledged. Rai even accuses her of hallucinating the whole incident. Instead, lore of the rock humans is given by a narrator chapters later, so no one hears it.
Rai will conduct a stealth investigation on Jobin (dropped)
After Ozone Baby, Rai says he's going to investigate Jobin as the one who lit the fire on the orchard, but after killing Wu, he and Josuke tunnelvision into the Head Doctor having the Rokakaka branch and are on the run for days after Josuke "kills" a passerby because of WoU. Jobin and Rai also die later.
Holly created the rokakaka lab and failed in her research of the plant (dropped)
Revealed by Wu Tomoki but never elaborated on. How she discovered the rokakaka or why she was researching it before Yoshikage Kira even knew about its existence remains unexplained.
If a person's heart changes, so does their Stand (dropped)
The closest thing to this is Tsurugi (the focus of the flashforward when the phrase is stated) using his Stand on bystanders during the WoU arc around the time he starts doing questionable shit with Jobin. Later on, it's revealed to just be a mix of calamity courtesy of WoU and his Stand glitching because of the rock disease.
Go Beyond can even overcome curses (dropped)
Rai's ghost states Josuke's ability can overcome curses just like how it can overcome calamity. However, the Higashikata's curse is broken by equivalent exchange with the new Rokakaka, the only thing Josuke does being exploding the shit out of Tooru from afar, and Holly's "curse" (which as stated above was retconned not to be one but an attempt by the rock human doctors to silence her) is never broken.