"Pokémon that are holding Berries or other items cannot be deposited into Pokémon Bank, and it is advised to return any held items to the Bag prior to depositing Pokémon. If the player attempts to deposit Pokémon that are holding Berries or other items, the items will be removed and sent to the player's Bag. Items held by Pokémon being deposited into Pokémon Bank will disappear if the player's bag is full."
White Kyurem and Black Kyurem can also not be transferred over to Pokémon X and Y using Pokémon Bank. As White Kyurem is a combination of Kyurem and Reshiram fused together and Black Kyurem is combination of Kyurem and Zekrom fused together. Therefore you would be transferring two Pokémon for one so Kyurem, Zekrom and Reshiram must be transferred separately.
There is also a limit on "hacked" Pokémon that can be transferred to your X and Y using Pokémon Bank. Most commonly Pokémon who don't have a legitimate ability, moves and stats etc.
Pokémon that have HM moves such as Surf and Fly are not restricted and can be transferred over with no problem what so ever.
Source: Knowledge and Bulbapedia
Hope I helped :)