That summary is kinda awkward, but I couldn't think of a better way to phrase it

To reproduce

1. Save the following configuration as a structure: 
   
2. Load the structure back into the world someplace underneath the open sky, and notice that the mushroom isn't there

If you generate it somewhere where the location of the mushroom is already dark enough for a mushroom to be placed, the mushroom will place successfully.

The problem seems to be that the game isn't taking the other blocks in the structure into account when trying to place the mushroom.

For further proof that lighting is the problem, try replacing the stone underneath the mushroom with mycelium and note that it generates just fine.