In the Custom list, the user added a "no owner" filter. But the custom list still showing User stories with owners.
The filter is working as designed. The filter checks the User Story for the owner as well as its associations. So if the User Story contains a task without an Owner, the custom list will display the items even though the User Story has owner info.
For Portfolio Items, this works a little differently. If the settings for the Custom List are at the Portfolio Level (example: If the type = Initiative in the settings of the application), only Portfolio Items below Initiative will be searched. The Custom List will not search for artifacts under Feature (or bottom level Portfolio Item) level.