Do you have update data for your game installed? You're likely running the latest version of ORAS (v1.4) with a dump from the game (no update data, v1.0). If there's a mismatch between what's installed (1.4) and what's on your SD Card (1.0) in terms of ExeFS and CROs, the game will crash.
Either dump the 1.4 update data and use that in your editing process when using pk3DS, or delete your game's update data and run the 1.0 data.