Microsoft has just released the following KB Article:
You cannot remove a prestaged package on a distribution point in System Center 2012 R2 Configuration Manager
Symptoms:
When you try to remove a package that was prestaged to a distribution point in Microsoft System Center 2012 R2 Configuration Manager, the package is not removed.
Note This problem occurs when the Copy the content in this package to a package share on distribution points option is enabled.
Full details at:
https://support.microsoft.com/en-us/kb/3031967