You can access Luma3DS Menu by holding "select" button on boot, enable "Game patching" and hit start.
Ok, that means it's something with the cartridge. I'd suggest downloading the digital version (and install it with fbi), it has to be the same region as your cart, backup your save with Checkpoint and restore the save once you install it. Note you have to launch the game atleast once for the game to appear in Checkpoint.
It's worth a try, if your cart was the issue, this problem wouldn't occur when using the digital version.