You can get crystal shards in one of two ways:
Every 500 Rhythmia will give you a new unlock option - you'll get the occasional shard that way (but not often, since there are also unlocks for the movie theatre, music player, and twelve other playable songs that can appear here).
Playing through the Chaos Shrine mode and defeating the bosses there is the more reliable way. Doing well with a fast party member on the first (FMS) stage determines which boss you get, and having enough attack power to defeat the boss on the second (BMS) stage will get you items. The higher number bosses tend to have crystals as their "loot drops" more frequently.
Once you find a Chaos Note stage with a boss holding a crystal you need, simply play that stage repeatedly until you have all eight shards of that color. Svenyip - 8 years ago
It seems the fastest way is through the Dark Notes. After you beat certain boss movements it will tell you what they drop, and then as long as you kill the boss each time you will more than likely get one. Noctis72 - 8 years ago