Extra are files those that Calibre lost track of.
ANYTHING that changes the folder or File Names (inc case), is an issue (Another reason Network, cloud filesystems calls issues, this include Humans
Look close to the (errors found) List. for ever Missing, is there ALSO an Extra with a similar name? A sure sign of file system being tampered with by something. The only safe way, is to use Calibre to: Add, rename, Delete books