I baked pots de creme au chocolat yesterday following this recipe, but something went wrong:  As you can see in the photos below, the chocolate seems to have separated out, forming a relatively firm top layer, while the remainder underneath is lighter in color and has an unappetizing wet mousse-like texture.    I followed the recipe closely, but let me add some clarifications to avoid ambiguity:   I made the chocolate variant only, so doubled the quantities of dark chocolate (I used 65%) and cocoa I beat the eggs and sugar in a stand mixer with a wire whisk attachment, then added the infused milk and then the melted chocolate while still mixing on low speed I poured the resulting mixture into eight 4oz glass canning jars (~3oz per jar). At this point, the mixture appeared to be homogenous. I arranged the jars in a 9x12x2" steel pan, placed it into an electric oven preheated to 320 degF, then filled the pan with boiling water to about halfway up the glass jars.  I baked these until the tops would hardly wobble when I tapped the jars, which was at the 29 min mark 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. After cooling briefly, I put lids on the jars and refrigerated them for several hours. The photos above are after refrigeration overnight.   The only possibility I can come up with is that I inadvertently filled the pan with cold water. I used an electric kettle, and while I thought I heard it bubbling in the background, my attention was focused on another recipe. Maybe I never switched it on.  Is this a likely explanation for these results? I can see how a cold water bath would result in uneven cooking, but I haven't been able to find good reasoning for why the chocolate would separate out on top. 
I'm relatively confident I have figured out what went wrong with these pots de creme au chocolat.   I tried this recipe again, and this time I mixed the chocolate a different way to see if it solved the problem. Instead of melting the chocolate first and then adding it to the eggs, sugar and milk mixture, I chopped the chocolate first, then poured the hot milk over the chocolate while stirring.  I noticed that this chocolate and milk mixture never became completely smooth. There were many granules of chocolate (about the size of granulated sugar) floating in the mixture, which would not dissolve, even after prolonged stirring. Tellingly, when I stopped stirring, these granules floated to the top of the milk, forming a layer that was clearly visible through the side of the bowl.  In hindsight, I noticed these granules when I attempted this recipe the first time, but didn't appreciate what they were or that it was abnormal. I found a reference to this issue here:     If your recipe calls for melting chocolate with a liquid, such as   cream, again, the proportions need to be right. Too little liquid, and   your chocolate will separate and look horrible (this can usually be   corrected by adding more liquid). If you have too much liquid and   don’t add it slowly enough, however, you may end up with small   particles of chocolate suspended in it.   It looks like this applies to both methods I used to mix the chocolate with the milk, since a large volume of liquid was involved in both cases.  I was able to solve the problem using a handheld mixer on high speed to beat the chocolate and milk, which broke up the granules and gave a smooth mixture. I then added this to the egg and sugar mixture and proceeded with the recipe, which produced homogenous, perfectly-cooked pots de creme au chocolat!  So, to conclude, I'm confident the problem was that the chocolate didn't mix fully with the milk, resulting in chocolate granules that floated to the top of the mixture, forming this chocolate-rich layer on top of the pots de cremes. I It should be possible to prevent these granules forming by melting the chopped chocolate with a smaller amount of milk (but enough so that it doesn't seize), and if you get granules, they can be broken up by beating with a handheld electric mixer on high speed. 