We keep experiencing an issue here, and I'm not sure whether it is a NuGet issue or a P4 plugin issue.
Whenever changes are made to packages referenced by a project, the csproj file is checked out of P4, but the packages.config is not.
This means that a dev checks in changes that then fail to build on any other machine.
As the csproj is successfully checked out, I am assuming that the changes being made to packages.config are being done directly to the file rather than through any sort of VS interface.
If you remove a NuGet package from a project and this happens to leave the packages.config empty, the P4 plugin successfully pops up to ask if you want to mark it as deleted in the depot.
The P4 plugin is configured to automatically check out any files without confirmation, etc.
If you need any further info, let me know.