Nintendo has offered a tiny update to The Legend of Zelda Majoras Mask 3D for Nintendo 3DS on the e-shop. 

To my knowing this update fixes the small amount of glitches that have been found in the game.

This update does not change any saved data at all. Once you updated the game it will state 1.1 in the title screen before you start playing.  Sadly the game doesn't support Lz and Rz for masks or items, which is something I really want to use in my New 3DS. I don't believe this update is required to play the game so if you like the glitches you might be able to keep them by not updating.

 Update on this story 3-2-2015

Nintendo has given some details to this Majora's mask 3d update that I have attached below: 

• Fixed the issue in which an “ERROR!****” message appears in-game
• Fixed the issue in which users become unable to swing their swords after playing at Honey and Darling’s Shop
• Adjustments have been made to make for a more fun gaming experience

Notes:

• You can still use previous save data after downloading this update.
• Update data will be saved on the SD Card that is inserted into the system.
• If there is not enough space on the SD Card, the update will not be completed.
• In order to check available space, select "System Settings" from the Home Menu and then select "Data Management."
• After download the update, please do not delete the update data. Update data can be viewed in the "Downloadable Content" area of the Data Management menu.

Source : Nintendo