top-level items only not working on saved search

I have some saved searches set up to look for items that either do or do not match a series of tags.

This was working well but recently some greyed-out items have been appearing in my search results. I am not exactly sure when the problem started occuring.

I searched the forums and found that this might be because I don't have "show only top-level items" ticked in my saved searches.

I checked and I *do* have that box ticked, however the search is still picking up linked attachments (which I linked with zotfile) that it thinks are not tagged.

Any suggestions as to what else could be going wrong for me? If I haven't explained this properly please do let me know.
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