Many causes can prevent you from filtering when using Content Matrix SharePoint Edition built-in filtering
For starters, Content Matrix uses inclusive filters - that means, if you specify "Name" Must equal "Document Library" it will include that library in the copy.
If you'd like to Filter Out, you'll be required to use "Must Not Equal" / "Must Not Contain" conditions.
If you want to specify more than one library / list to filter out - use the AND operator after each statement.
For more details - you can reference the Content Matrix Edition User Guide:
Filter Options
