I have the problem also. "Sample File Parameter2 (2)" is supposedly referencing a query that I didn't created, but there is no such parameter and not one single shred of Power Query code references the query or the parameter.
The problem is the result of using some of the transformations available on the toolbar to filter the data. These transformations created multiple folders of queries, some of which could be deleted, and some of which can't. It is absolutely a bug somewhere in Power BI.