As Dani says, if you put the second layer in to soon it will run in and blend with the level below - when my grandmother died we found a candle I had made when nine years old which she had kept - it was a square block candle which (if I remember correctly) was supposed to be two layers, one blue and one yellow, but in fact it ended up being dark jade green at the base, slowly changing to amber at the top!!
same then, if you let one layer cool too much, there's the chance (As per Dani) that the next layer will leach into the gap created as the candle contracts or (especially with pillar candles) that the two layers don't bond together properly.