This rumor came to be after the Spanish site Meristation published an interview with Pokémon designer Mana Ibe in which it was denied that there would be a third version of Pokémon Black and White. Junichi Masuda stated that he did not recall ever saying there would not be another version, and that he was very surprised to hear about the rumor.
It is unknown why Mana Ibe and Junichi Masuda did not make similar statements. The former was also present during the more recent interview with GameTrailers, but she was not asked about her previous comment.