Well, I have some fixes for you to try.
First verify that your Nintendo 3DS console is in the latest firmware (11.15.0-47X).
You can check in the System Settings app on the 3DS, at the bottom right side of the screen. If the numbers don't say 11.15.0-47X (where X is whatever letter of U, E and J) just perform a system update.
The first fix (if the above steps didn't work) is to try and update the seed of the game.
Here are the steps:
- Verify that your FBI installation is the latest (2.6.1). If not, update.
- Connect your console to the Internet (if it isn't),
- Open FBI.
- Select the sub-menu Titles.
- Select in the list of games, the game you're having issues with.
- Select the option Import seed.
- Press the button (A) to accept.
Then you can try again.
If it doesn't work, then you would have to try this other fix:
- Retrieve the SD card from the 3DS.
- Move every file from the 3DS SD card to somewhere safe in your PC.
- Performe a format to your SD card with guiformat, selecting the option for unit size to 32768.
- After the format, follow this guide to verify the health of your SD card.
- If you get a Test finished without errors result, move all of your files back to your SD card. If you got any other result, your SD card health isn't good and you should get another one to replace it.
This should —to some extend— help if your error is kinda generic.
If none of this works, then this issue would need some more involved methods to fix.