How are you playing the game? Is it a digital download version from the eShop? If it was a CIA it could be possible it was a bad dump.
The first thing I would recommend trying is if you still have the CIA, backup all the files on your 3DS SD Card, & then reformat your SD Card. Then restore the files back to the SD card from the backup you made on your PC. After doing this, use Checkpoint to backup your game save data & dump your own copy of the game using Godmode9 and try re-installing the game, then use Checkpoint to restore your game's save after launching the game once.
Make sure you are using the latest version of your Custom Firmware if you are using CFW, and make sure any cheat plugins are disabled if any are enabled as some cheat plugins may cause the game to behave strangely.