The solution I took was to change FxCop’s settings to ignore versions when resolving references

Reference resolution with Code Analysis/FxCop – TechBlog

Solves an issue with FxCop when you have a two NuGet installs that depend on different versions of the DLL.

Warning looks like:

The indirectly-referenced assembly ‘Newtonsoft.Json, Version=4.0.4.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed’ could not be found. This assembly is not required for analysis, however, analysis results could be incomplete.

This is a example raised by FxCop concerning Cassette.