NuGet is just great tool for the managing third-party assemblies in your Visual Studio projects. If you are using the ReSharper and you are using a type that isn’t referenced in the current project but in another one, ReSharper will offer to add new reference just with the one click. In the case of NuGet, those assemblies are indeed referenced from the right location, but are not using the packages.config metadata file, which is essential for the NuGet to know which assemblies are referenced by what project.

But is seems there is already for a couple of time a solution for this. JetBrains (the company behind ReSharper) released plugins for ReSharper 7.1 and 8.0.

If you want to know more details about the issue read here.