To reproduce (if using user project, just open it):
1. Create a new Unity project.
2. Create a new custom vs solution, add generated default csproj.
3. Create new c# Project within the cusotm solution, for instance to contain a Unit Test. Save the project in any subfolder in root project directory, NOT in Assets folder.
4. In Visual Studio, right click the new Tests project, and select "Manage Nuger Packages".
5. Add a 'NUnit' nuget package to your new project. A new 'packages' folder will be created in root direcotry of the project, where the downloaded nuget package will be stored.
6. Go back to Unity. Unity will scan the new 'packages' folder, mark all files as assets (metadata files will be created).
7. Unity complains with a compilation error related to the duplicated NUnit assembly. The assembly is not used at all in any script Asset across the project, yet the project wont compile:

Reproduced in 2017.2.0b4, 2017.2.0b5, 2017.2.0b6, 2017.3.0a2
Not reproduced in 2017.2.0b3, 2017.2.0b1, 2017.2.0a1, 2017.1.0p2