Moogle are Beastmen, they hold authority over the Black Shroud and now they are pissed at random Silver Clad Generic Empire burning down their home and stealing their flowers (You know, (A Moogle Banquet)). So they summon their Primal and strike back at filthy lowly "non-beastmen". Don't mess with the Moogle Dynasty.

Actually, if you do the side quests/class quests you can see Moogles are being treated unfairly despite being the boss of Black Shroud. Enough is enough >_>