Revised Era is generally agreed to be the worst offender, as while many enjoyed the mechanical changes, others thought they were needless complications (especially to the already bulky combat rules) such as the division of Bashing/Lethal/Aggravated damage rules and the dice splitting systems.
Crossovers between the games are this as well. White Wolf was notorious for providing ways that games could crossover while being extremely unhelpful when it came to to actually place their ruels or cosmologies together in a single cross over game. This has led to a sizeable number of fans who outright refuse to use the splats as written in one game interact with another as written in its own corebook. Such as The Garou from Werewolf: The Apocalypse interacting with Awakened Magi from Mage: The Ascension. While others very much enjoy being able to play a Dreamspeaker mage fighting alongside (or against) a Silver Fang.
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.