Generally, the brown coloration indicates the prescence of 3,4 methylenedioxy-phenyl-2propanone,aka MDP2P, which is the direcr precursor of mdma/mda.
The reason why it's in the crystals is simple, and as always, based on economics. MDP2P and MDMA's boiling points are very close together, with mdp2p's slightly higher.
As the distillation finishes, the temperature in the distillation flask rises, and as it does so, mdp2p begins to come over WITH mdma.
MDMA is an off white oil, and MDP2P is gold, to brown, depending on the reactions that produced it, but regardless, it is brown when found in crystals.
MDMA, being an amine, will form a salt when reacted with an acid.
MDP2P, being, chemically, a ketone, will not, but crystallization of a mixture of mdp2p and mdma will make brown crystals.
The brown is removed with an acetone wash. Acetone is a ketone,too,
but it wont disslove crystallized mdma unless theres water in the acetone.
However, it's really not good economics to get too persnickety in purification, as the point of diminishing returns is reached quickly after a wash or two. Foe my own personal, however, I liked 'em blinding white.
Your body still has to process ketone for detoxification, so it's not exactly a good thing for it too be in there.