Patches for Pokémon X and Y and Pokémon Omega Ruby and Alpha Sapphire are now available to download off via the Nintendo eShop. The version 1.4 patch for X and Y as well as the version 1.3 patch for Omega Ruby and Alpha Sapphire both officially state that: "Various bugs have been fixed to provide a smoother gaming experience." (ゲームを快適に遊んでいただけるよう、いくつかの問題を修正しました。)

The patch is required to play in all official tournaments as well as any online play. It has been reported though that the patches block the injection hack that players have been using lately on legitimate official Pokémon carts.

XY Version 1.4 QR Update Codes

ORAS Version 1.3 QR Update Codes

Sources: http://www.nintendo.co.jp/3ds/ecrj/update/index.html and http://www.nintendo.co.jp/3ds/ekjj/update/index.html