I had the same issue.
When I ran nuget restore for sln:
> nuget restore MySolution.sln
MSBuild auto-detection: using msbuild version '14.0' from 'C:\Program Files
(x86)\MSBuild\14.0\bin'.
All packages listed in packages.config are already installed.
When I ran the restore command individually for each project in solution:
> nuget restore MySolution.Common\packages.config -PackagesDirectory .\packages
Restoring NuGet package Microsoft.Azure.KeyVault.WebKey.3.0.0.
Restoring NuGet package Microsoft.Rest.ClientRuntime.2.3.13.
Restoring NuGet package Microsoft.Azure.KeyVault.3.0.0.
Restoring NuGet package Microsoft.Rest.ClientRuntime.Azure.3.3.15.
Restoring NuGet package NLog.4.5.9.
Restoring NuGet package Autofac.4.8.1.
Restoring NuGet package Microsoft.WindowsAzure.ConfigurationManager.3.2.3.
Restoring NuGet package System.IO.4.3.0.
....
All references are back, and the solution builds correctly after this.
Seems like a Nuget bug.