Repro steps:

1. Open Unity and create a new project
2. In the project create a new c# script ( Assets -> Create -> C# Script)
3. Open the script with Visual Studio 2017 Community
4. In Visual Studio click on View -> Error List
5. Click Build -> Rebuild Solution
6. See that in the "Error List" there are 2 Warnings

Expected result: For no warnings/errors to happen
Actual result: 2 warning messages appear

Reproduced with: 2017.1.0b5, 2017.1.0b4, 5.6.1f1
Regression introduced in: 5.6.0f3
Not reproduced on: 5.5.3p3

Fixed in: 2017.1.0b7

Note:
Added video

The primary reference "UnityEngine.TestRunner" could not be resolved because it has an indirect dependency on the framework assembly "System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" which could not be resolved in the currently targeted framework. ".NETFramework,Version=v3.5,Profile=Unity Subset v3.5". To resolve this problem, either remove the reference "UnityEngine.TestRunner" or retarget your application to a framework version which contains "System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a".

The primary reference "nunit.framework" could not be resolved because it has an indirect dependency on the framework assembly "System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" which could not be resolved in the currently targeted framework. ".NETFramework,Version=v3.5,Profile=Unity Subset v3.5". To resolve this problem, either remove the reference "nunit.framework" or retarget your application to a framework version which contains "System.Web, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a".