I can’t reproduce this behaviour. Would you be able to list the files/directories that this is affecting?
The only .NET location targeted by System Ninja are:
DetectFolder:%WinDir%\Microsoft.NET\Framework\v4.0.30319\SetupCache~|*.*~|RECURSE
DetectFolder:%WinDir%\Microsoft.NET\Framework64\v4.0.30319\SetupCache~|*.*~|RECURSE