Reproduction steps:
1. Open project attached (ShaderDefaultTextureIssue.zip).
2. Select material_1 from "Assets/Materials".
3. Press "Select Dependencies".

Expected result: Only one texture will be shown.
Actual result: Both textures will be shown.

Note: Material (and shader) used to have 2 textures, but after editing shader, second one were deleted from shader script. After that, material still select both textures as dependencies.

This is how to recreate this situation from scratch:
1. Create a shader with two textures.
2. Assign two different default textures to the shader.
3. Save the project.
4. Comment out the second texture in the shader.
5. Save the project.
6. Do reproduction steps.

Reproduced on: 5.4.0f3, 5.5.3p3, 5.6.1p1, 2017.1.0b5.