These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Unfortunate Implications: World of Darkness: Gypsies portrayed the Roma peoples as having magical powers tied to how "pure" their blood was.
Villain Sue: the Old WOD was often heavily criticised for having incredibly overpowered antagonists and side characters, who had the potential to make the players irrelevant. Samuel Haight was the worst: the books actually told Storytellers to make sure that the PCs don't have a chance to defeat him.