Any chance it was condensation, and not a leak? I had one occasion where the inside of my ID Salathe let the foot of my sleeping bag get wet. Since I was using it under an ID Silshelter, and we had only a slight shower, I knew the bivy didn't leak. Turned out that, by having the shelter pitched low and the bivy pretty well closed, I allowed condensation to form inside the shelter and inside the bivy. It was user error, not equipment failure. I learned, too, that sometimes conditions make it very hard to use a bivy and avoid condensation - not impossible, but hard, which sometimes leads to less-than-optimal results.

If it was raining hard, is it possible that the surface of the waterproof-breathable material was effectively "sheeted over," so that vapor from inside couldn't escape? I know that gore-tex jackets, at least in the early days, had this problem when they "wetted out."