Author Existence Failure: The original manga was never finished due to Ishinomori's death. Thus, the final planned story arc, "Conclusion: God's War" was never finished or published in manga format in the year 2000 as Ishinomori had hoped for (as his death cut the planning short). That is, until 2012, when Ishinomori's son Jou Onodera used his notes to complete it as a novel (with the anime writers having previously adapted it as a mini-arc and OVA). It has now been completely adapted into manga format and published on Shogakukan's free manga hosting website. Do keep in mind that this is all happening only in Japan.
However, Ishinomori's planning notes are also said to differ from both Onodera's novel and manga adaptations to various extents, leaving it iffy on how faithful the final story may be at delivering on his intent.
Cross-Dressing Voices: 007 was voiced by Machiko Soga (AKA Bandora/Rita Repulsa) in the 60's anime and movie. In the rest of the anime adaptations, he was voiced by male actors. However, as the '60s anime adaptations had redesigned 007 to be a child (see below), a female voice was probably considered more fitting.
Ivan is a case of this in all incarnations of the anime, though it's averted in the English dub of the 2001 series.
Executive Meddling: In the 60s anime adaptation, 007 was turned from a forty-something former actor into a nine-year old Bratty Half-PintMouthy Kid who was functionally 009's Kid Sidekick along with Plucky Comic Relief. Ishinomori didn't care for this change, but had to incorporate it into the manga to some degree. The kid version of 007 got used briefly as a Mythology Gag in the 2001 anime adaptation, in a scene where 007 kept shapeshifting through different forms.
The continuation of the manga past the Underground Empire arc came from this and fan outcry; Ishinomori had to retcon the Bittersweet Ending and start a new tale with the cyborgs.
The Mythos arc's abrupt end came about when a new editor-in-chief was hired for Weekly Shonen King and ordered Ishinomori to wrap up the story as it was being dropped from the magazine soon. The editorial department had felt that the story and large amount of characters would be too confusing for children to follow.
The anime version of "Conclusion: God's War" was truncated to two episodes in its run on TV, with episodes 50 and 51 being cut and merged together. The DVD shows the episodes as they were intended to be seen.
Flip Flop of God: While the '60s anime was running, Ishinomori incorporated 007's child persona into the manga by having Gilmore upgrade him. First introduced as a permanent new form, it later flitted between Sleep Mode Size to a Super-Deformed mode for comedy moments (during the Underground Empire arc) to being discarded and forgotten entirely and back again. A Whole Chapter Flashback that Retconned their escape so that 007 was already in child mode (or just flat-out a child) didn't help, either.
God-Created Canon Foreigner: Hisui Kagariya (the girl who appears in the final arc of the 2001 anime) may seem like she was a character exclusively created for the anime version of "God's War", due to the fact that Ishinomori's notes had yet to be adapted into a manga format. She did in fact exist in the drafts for the arc, but would not make her transition to the intended manga format until 2012.
Hey, It's That Voice!: The dub of the 2001 series has many of these, even some in the exact same voice that some actors may have been known for in other anime dubs. Take any voice and look it up on Wikipedia and there will be a full list of roles that the voice actor has performed. Some will be more familiar than others.
Keep Circulating the Tapes: Only the first eight episodes of the entire 2001 anime were released on DVD in the US (the UK and Australia were a bit more fortunate and got the entire first half). Outside of bootlegs and internet uploads (which still don't cover the episodes after Episode 34, Episodes 38 & 46-48 not withstanding), the rest remain elusive. And only ten manga books have been translated into English, with Tokyopop's release only covering up to the end of the Underground Empire arc (which itself was going to be the original ending to the series).
Missing Dub: The English dubbed versions of Episodes 34-37, & 39-45 from the 2001 series are usually this. Episode 48 also only got to air in overseas broadcasts. As far as "God's War" (49-51) goes, the episodes were dubbed but remain elusive. The English scripts (complete with edits) were further adapted and utilized for the Latin American dub.
The Other Darrin: As far as the dub for the 2001 series goes, Joshua Seth was unavailable to voice Joe in episodes 5 and 9, with Derek Stephen Prince filling in for the role.
The '68 series recast the role of 004 at episode 18, with his voice actor switching from Hiroshi Otake to Kenji Utsumi.
Screwed by the Network: All but the last five episodes of the 2001 series aired on Cartoon Network. The first twenty-five got rerun in the Toonami block several times, while the rest were eventually aired during the Midnight Run. Once. They stopped right before the end of the Pu'Awak arc, deciding not to air the finale or the God's War arc. This meant the scene viewers were left with was 004 screaming Viina's name after seeing her and her sisters shot by Von Bogoot. Rather curious, considering that other Cartoon Networks (like CN-Latin America) exhibited the WHOLE series, God's War arc included, around a year before this happened.
Talking To Herself: The five Pu'Awak Sisters were all voiced by Yuki Masuda. This trope was averted for the English dub and the Latin American Spanish dub (with each sister being voiced by a different actress).
What Could Have Been: As mentioned in the Aborted Arc trope, "Angels" was originally going to be an arc to wrap up the manga, but it was unfortunately cut off on a cliffhanger when the magazine it was running in (Adventure King) dropped Cyborg 009 as a feature due to Ishinomori falling into a writer's block and being unable to continue the story. In the cliffhanger, the cyborgs learn that Ivan has the ability to upgrade them. The volume release of the Angels arc also had a footnote by Ishinomori, suggesting that the arc was difficult to write for due to him planning it to be the longest (and final) battle that the 00 cyborgs would experience. Ishinomori attempted to rewrite and revisit the storyline a few years later with "Battle with the Gods" (with it serialized in COM), but that was also cut short when the manga was dropped again- in light of fans' enraged letters over Joe and Francoise having sex and criticisms of Ishinomori's art and narrative style in the arc.
Before "Angels", the Underground Empire arc would have ended the manga with the now-iconic and infamous "shooting star" sequence. Before that, fans believe the Mythos arc was meant to be an earlier wrap-up, as the arc ends very abruptly with an explosion and a narration stating that there were no traces of either Cyborg team left behind (leading to the assumption that the 00 cyborgs were all dead). However, in that case, the destructive and abrupt ending was due to the manga being dropped from Weekly Shonen King, and Ishinomori not being given enough time to write out a more detailed finale.
Early draft designs for the characters had Jet/002 lacking the Gag Nose that he'd become known for, and Francoise/003 went through having several different hair style ideas before Ishinomori settled on her final look. Ivan/001 also lacked his Blinding Bangs, while Dr. Gilmore could have had an afro.
The Mythos cyborgs were originally going to appear in the 1979 series in an arc after the Neo Black Ghost one, and three episodes were being drafted while Ishinomori was drawing redesigns for the characters. Unfortunately, the '79 series was cancelled at episode 50, leaving things to be hastily wrapped up with the Neo Black Ghost arc. Not all was lost, as the redesign for Helena/Artemis did eventually make it into the 2001 anime.
The 2001 anime was originally tended to stick a lot closer to the manga, with only Birth through Underground Empire being adapted (thus no recap episode, "God's War", or the later manga stories that were placed earlier in the chronology). The pitch trailer included the Accidental Murder in 002's backstory that was entirely removed in the actual anime. Helena/Artemis also appeared as a blonde as she had in the manga. However, 008's original controversial manga design was also present, leading to him to be redesigned in the final product, likely so the series would be able to be released overseas. 008's home country was also given as "Kenya", as opposed to the fictionalized Muamba Republic that was used in the final product. If the other profiles were also indication, the cyborgs' backstories were considered to undergo modernization or had some errors that were later fixed, with 004 being said to hail from "former West Germany" (when it was a point in the manga that he was East German).
Within the first drafts for "God's War", Hisui Kagariya originally had the given name of "Igusa", and her age was also given as 24 instead of 27. In addition, Shiori Takagaki had the given name of "Saori", and an altered version of Joe's backstory was to be detailed (where we would learn his mother's name).
Archaia's graphic novel of Cyborg 009 was labeled "Ishimori Universe, volume 1", suggesting that there were plans to adapt Ishinomori's other properties and create an expanded universe featuring all the different characters. This was confirmed at Emerald City Comic-Con 2014, where it was revealed that Android Kikaider would have been the second graphic novel release, followed by other titles (which included a sequel Cyborg 009 novel). The different Ishinomori characters would then form an Avengers-esque alliance. Sadly, due to a change-over in staff at Ishimori Productions, the plans for further graphic novels fell through.
The company "Comic Book Movies" had planned to do a live-action film adaptation, as well as a Western-animated adaptation. Both plans fell through, though the concept art for the latter was designed by Peter Chung and can still be seen floating around online.