Continuity Snarl: There were quite a few retcons and quite a few mistakes. It's difficult to tell which is which.
Fan Wank: Several actually got noticed by the authors and mentioned derisively in the canon, among them a male offshoot of a female only Vampire bloodline, and a "pact" or "understanding" between Gangrel and werewolves, undermining the usual state of affairs.
Nightmare Fuel: Specific examples in the Old WOD: the Baali and the Sabbat in Vampire, the Black Spiral Dancers and the Wyrm in Werewolf, the Nephandi and Marauders in Mage, the Spectres and Oblivion in Wraith, the Shadow Court in Changeling, the Akuma and Yama Kings in Kindred Of The East... It's pretty much easier mentioning which factions are NOT Nightmare Fuel.
More specific examples from oWoD: the Nosferatu, the Nicktuku (Nightmare Fueleven to the Nosferatu), Followers of Set, the Giovanni, the Tzimisce and (to some extent) the Malkavians in Vampire, the Bane Mummies in Werewolf and the Earthbound (and pretty much any high-Torment fallen) in Demon.