fragmentation errors? Are you using Wood for M3?
If thats the case usually deleting the nds on the SD card (copy it back to your PC first if you dont have it there anymore) and then copying it back onto the SD should fix that. The same fragmentation problem might also occur to the save file of the game, the procedure is the same.
I don't recall the touchpod/sakura firmwares to have fragmentation errors, so I guess you are using wood, if not, then I don't know whats wrong.
If the copying stuff won't work, you might as well play Inazuma with the usual firmware or sakura, but then it needs to be AP patched.