Entire Base Layer Appears When it Shouldn't

This pertains to Scene 2 Slide 17 (2.17). I have a base and 2 layers (croissant and calzone) . The croissant layer displays properly as it includes the elements that I want to keep from the base layer. The calzone layer is fine at the beginning, but in the end it reverts back to all (which I don't want) the elements of the base layer.

What did I do wrong? 

2 Replies