In a dark note BMS, bosses are almost always the fourth enemy to show up.  If you defeat them fast enough, you can repeat the cycle and trigger a second boss fight..  But more often than not, you'll probably find yourself facing down the 3rd enemy of the second cycle when even a low level dark note ends.  Here's a solution: Use offensive skills with boss triggers (Bartz's Mimic, Cecil's Soul Shift, etc.)  My party setup is currently with Bartz and Cecil with the previously mentioned skills, warrior of light with focus, and Zidane with steal and treasure hunter.  By specifically playing dark notes with a boss 3 that is not an actual FF boss (they have lower HP compared to proper bosses), Mimic and Soul Shift can instantly kill them, quickly speeding up the enemy pattern.  It's enough to down 3 bosses per BMS depending on the song, and makes crystal shard acquisition much easier.

I agree with this, sometimes you can kill three bosses in one song.

However, the bastards don't always drop shards! I'm trying to farm Gray Shards from one particular boss, but the fucker just keeps dropping trashy items instead! It would be okay if it dropped other gems, but I've already completed the other two it drops.