You go through your third party updates and delete any expired or unneeded packages. The easiest way I found is to click on third party updates, then filter for updates with content and just see what you dont need
I have had the same issue in the past. The Wsus\UpdateServicesPackages holds 3rd party packages that have been published from Patch Manager.
I have a script that I use that looks for un-referenced packages and then adds them to a text file. Once we have a list in the text file we loop the file to remove the folders from the server.
You need to run the batch file as an administrator for this to work.