Nara Shikako (Dreaming of Sunshine) is also showing up under Naruto

Morgan le Fay (Arthurian Mythology) is showing up under The Squire's Tales Series - Gerald Morris

Several characters from Vampire: The Masquerade: Bloodlines are also showing up under Vampire: The Masquerade
Deb (Vampire: The Masquerade – Bloodlines)
Fledgling (Vampire: The Masquerade - Bloodlines)
Mercurio (Vampire: The Masquerade - Bloodlines)
Pisha (Vampire: The Masquerade – Bloodlines)
Sire (Vampire: The Masquerade - Bloodlines)

Some characters from Warhammer 40k (Novels) are also showing up under Warhammer 40.000--everything under Novels is meant to be there; no idea if they were also nominated for the other subfandom.
Angron (WH40k)
Fulgrim (WH40K)
Khârn (WH40k)
Konrad Curze (WH40K)
Magnus (WH40k)
Mortarion (WH40k)
Perturabo (WH40k)
Sanguinius (WH40k)

Unassociated characters:
Devon Adair (Earth 2 1994)
John Danziger (Earth 2 1994)
True Danziger (Earth 2 1994)