There are two main reasons your mousse could separate. The first has to do with the chocolate, and the second has to do with the egg whites. If the chocolate seizes while melting, it will be tough to whip with the rest of the mousse. That's why you want to avoid letting any water touch the chocolate as it's melting. Second, you want to make sure you don't overbeat the eggs. Otherwise, they could become grainy. I recommend beating the eggs until they form soft peaks, but you don't want them to become stiff peaks.