MDMA forms a number of hydrates when crystallizing, depending on how much water is present (Ref: Pihkal #109), meaning that a varying number of water molecules are incorporated in the crystal lattice along with the MDMA molecules.
If you fill a box with oranges and shake them, they form a certain pattern, with them stacked neatly in layers (this corresponds to a pure MDMA.HCl crystal). If you add a few dozen ping pong balls (representing water molecules) to the mix and shake, the stacking pattern won't be the same any longer, and the overall crystal shape will also be different. Hence, the crystallization conditions will heavily influence the crystalline shape.
Also see the discussion in this thread about solvent effects:
Post 398077 (missing)
(GC_MS: "3,4,5-trimethoxynitrostyrene xtal shape", Newbee Forum)