Is this copy of Omega Ruby installed on your SD card? Was it acquired from Nintendo eShop, freeShop, or that iso site?
Try backing up your game save through JKSM or Checkpoint, reinstall it again from a different sourced copy (or preferably eShop or freeShop), and restoring the save. Continue playing unless the issue occurs again.
You may want to back up your entire 3DS setup onto desktop, reformat the card, and run that card through H2testw if there's any underlying physical defectives.
Some games do have bugs that are prone to crashing. For example, Metal Gear Solid - Snake Eater 3D [the .3ds rom floating out there when converted to .cia] will crash without fail during this cut-scene of