WinSCP, and other clients, do this because they want to ensure that it's possible to distinguish between truncated uploads and completed uploads. In your case, it fails because the file is moved immediately after it's been uploaded and before the command to rename it is executed. The file, with the .filepart, extension will be moved by the process trigger event-handler and the rename command will therefore fail.
One way to avoid this is to use a regular expression file filter to ensure that the event-handler does not get triggered for files whose names have the .filepart extension. You can do this using the following filter:
This causes the event to trigger for any file underneath /Home whose name doesn't end with 'filepart'. You may of course need to change the path from /Home to something else. The 'regex:' at the front simply lets CompleteFTP know that the rest of the text is a .NET regex. You also need to enable the event for the 'Move file' event since the final operation isn't an upload but a rename.