Early in the game, it's stated that each Memory Core only spawns a new CPU Memory once every few hundred years. Noire and Neptune got their CPU Memories from the same Core Plutia got hers from. Plutia only recently became a CPU. So... a single Core suddenly spat out three CPU Memories in a row, while Vert got two of them from another Core, yet they're only supposed to spawn once every few hundred years? Why was Noire camping the same Core that Plutia's Memory came from when it shouldn't have spawned another one for centuries? Shouldn't she have been checking other Cores that last went off centuries ago?
Just where did Histoire and Croire come from, anyway? They seem to suggest they're something CPUs are just supposed to have as part of being CPUs, yet Noire, Blanc, Vert, and Peashy never get their own equivalents of Histoire and Croire.
Okay I'd like to point out Kei, Mina and Chika are Human and that Histoire and Croire are fairies. Also in the first game Histoire seems to have some godlike power as she was the one whoa actually created the CPUs (granted that was probably chocked into Canon Discontinuity by mk2, on the other hand a couple other elements form the first game resurface like Histy;s use of emoticons, the Nep-Ship and Neptune being the protagonist so...). I bet is that the Fairies have some power over history. as it was stated in canon, Histoire observes and advises and Croire directly interferes and changes. an analogy would that Histoire is the Time Lords and Croire is the Doctor.