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Calibre ignores files it doesn't know about. And if you change the title or author of a book, or move it to some other library, I suspect that the folder and the files typically will be orphaned.
There are some library maintenance functions that can be used to fix this. By fix I mean delete orphaned files. Or you could copy the library to a new location and the orphaned folders and files will be left behind.
But you should also try to avoid doing anything to the calibre library directly. Always use the GUI. Except when making backups of the whole library, of course.
Try to tell other programs to not create any files in the calibre library.
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