find the same "bug" with Photoshop CC 2014 - Classroom in a book - lesson 5
I opened the prepared file "Glass_Start.psd" and use Auto Align Layers, then used Auto Blend Layers,
The result is that the top layer have totaly black mask applied and the bottom all white.
I have try to switch the Layers, but with same result, (first=black mask/ second white mask)