Manually randomizing Pokémon Y is notoriously buggy. The game has anti-randomization checks due to the "Lumiose City save glitch" of the original game. A high-quality repack includes cheat codes (like the "Crash Fix" code for Citra) pre-applied.
Assuming you have downloaded a file named something like Pokemon_Y_Randomizer_Repack_NoCrash.3ds, follow these steps. pokemon y randomizer rom download citra repack
If you cannot find a reliable Pokémon Y Randomizer ROM download as a repack, you should do it yourself. It is surprisingly easy. Manually randomizing Pokémon Y is notoriously buggy
This method is safer for your PC (no viruses from repack sites) and gives you total control over the chaos. Assuming you have downloaded a file named something