Only Pokémon that were obtained through normal gameplay, or were distributed through an official distribution, can be transferred through Poké Transporter. If one or more of your Pokémon will not transfer, it is likely the result of third-party software manipulation. We recommend that Pokémon users only use Pokémon that they obtained themselves, as a traded Pokémon's origin cannot be verified with complete certainty.
Millions of Pokémon have been sent through Poké Transporter, and extensive information is maintained regarding all past distributions to ensure that any legal Pokémon acquired through normal gameplay or from any official distribution is able to be sent successfully.
Please note: Cosplay Pikachu is an exception and cannot leave Pokémon Omega Ruby or Pokémon Alpha Sapphire.
We cannot assist further in such matters and apologize for any inconvenience these restrictions may cause.