NCrunch is reliant on Visual Studio restoring Nuget packages for it. In the early stages of integration with .NET Core, NCrunch tried to do this itself, but it only caused chaos.
If you're seeing this consistently after resetting the engine, check to make sure you have a Nuget dependency on System.Collections.NonGeneric from your test project. NCrunch does have a known issue where it has difficulty negotiating some Nuget dependencies that are not referenced directly by the test project.