The first one I think Vander gives it to you.
The second one you have to use the U-Disk in the Under to get it.
I dont remember where was the other one.
~Lightning;rukario;
Oh now that I remember there isnt a third Time Flute.
~Lightning;rukario;
beat Mt.Battle in Story Mode and once you get to the hundreth trainer it should be ina box on ur left or right.