I have a SharePoint library with a large # of items in several document sets. There are many unique values in several columns to the point where the standard column filter menu does not appear, instead a link to "Show Filter Choices" appears in its place.
When this link is selected, the dropdowns generated appear to provide filter values in the context of the top-level view of the library instead of for the documents inside the document set as expected.
When this option is selected in a flat view or with the documents OUTSIDE of a document set, the filter choices appear in the dropdown filter as expected.
The columns in question are indexed & # of items returned is below the list item view threshold. Also, there is no special view configuration - the same view is used throughout the library. I was able to re-create the same issue in my local & development environments. Below are screenshots of the issue.
Top-level view, note that the document set was modified by the system account, this was intentional & significant in the next screenshot:
Screenshot of the column filters, the "Document ID" filter only has "(Empty)" as an option presumably because the document set doesn't have the "Document ID" property.