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If you haven't gotten the upgrade to Moogle Hunter, continue on in Bresha Ruins until after the monster party member battle, go to near the Time Gate and Moogle will glow and fly off towards a soldier. Talk to him and then you'll have the ability to reveal the spheres.
Official Guardian Ancient Robot of the Knights of Safe Haven Playing: Ocarina of Time 3D, Super Mario 3D Land, Mario Kart 7