They don't show in the details panel, either, so #2 is correct.
If we assume you have tapped O (open containing folder), and there IS a book of the format missing:
It got there by bypassing Calibre.
or
Someone synced the metadata.db while calibre was running (and it synced in the wrong direction). So you ended up with a DB that had a copy, but the copy did not come with it. IMHO Managing by sysnc is fraught with these issues.
Always disable sync while using the GUI. Better yet, Only Shadow sync (make a copy) of the Master Library
Bottom line: Run Library Maintenance. Fix the issues. Stop doing that what broke it in the first place.