Jossed: Much misinformation has been spread about the series' storyline due to it not being well known overseas. Some of the things that has been considered canon by fans are:
Myth: "Sharon and Blair are sisters." / Truth: Blair is the heiress of a wealthy European family, while Sharon was orphaned as a child and never knew her true parents.
Myth: "Hokuto and Hayate are lovers." / Truth: Hokuto and Hayate have nil to do with each other, although Hayate does end up being paired with a shrine maiden in his Japanese EX2 ending.
Myth: "Skullomania and Shadowgeist are twin circus performers." / Truth: Skullomania is a Japanese businessman, while Shadowgeist is a vigilante from an unknown dystopian nation.
There's another myth that Shadowgeist is Skullo's evil supervillain of an older brother and the heroic Skullomania must put him down. Again, untrue (despite the similarities between their movesets). Plus, Shadowgeist is an anti-hero at worst.
Myth: "Kairi kills Akuma." / Truth: "Akuma simply disappears from the series, with no explanation given for his absence."
Myth: "Garuda is Goutetsu's third student." / Truth: "Originally Garuda was an evil spirit created from the souls of fallen warriors killed by the Satsui no Hadou, but he was later retconned into an evil spirit created from humanity's negative emotions."
Myth: "Hayate was killed off, which is why he doesn't appear in EX2 Plus and EX3 / Truth: "No explanation was ever given as to why Hayate was removed from the series."