I think this is a bug, there should be no reason for two identical .nupkg files in a package folder.
Using NuGet v3.2.60902.10488 in VS2015.

Repro steps
Create a Console Application
Install-Package MvvmLightLibs.5.2.0.0
Inspect the packages folder for MvvmLightLibs

Expected:
There should be only one MvvmLightLibs nupkg file and one CommonServiceLocator nupkg file in the CommonServiceLocator.1.3 folder.

Actual:
There is MvvmLightLibs.5.2.0.nupkg + identical MvvmLightLibs.5.2.0.0.nupkg file in the MvvmLightLibs.5.2.0.0 folder and CommonServiceLocator.1.3.0.nupkg + identical CommonServiceLocator.1.3.nupkg in the CommonServiceLocator.1.3 folder.