What went wrong with these pots de creme au chocolat?
You've answered your own question. The water bath should have gone all the way up to just above the crème in your pots. I'd also bet that you had this on the top rack of your oven, this type of water bath should be on the lowest rack to keep the tops from cooking faster than the bottoms which is what looks like happened. I've had the same thing happen with crème brulee before.


  Once I removed the jars from the water bath, the layering was
  immediately obvious in all eight pots de creme. Interestingly, the
  bottom of the chocolate layer seems to roughly align with the water
  level in the bath.