If its a cia version from the eshop. Its cryptofixed. Make sure to go to the e shop and load the pokemon yellow page. The game should boot up afterwards
I've ran into this issue on a couple of systems. I'm not sure if this works for everyone but I deleted the .cia with BigBlueMenu and then opened up the eshop and it let me redownload it straight from the eshop instead of installing the .cia with BBM