Try running calibre's database check. Click the "Library" button, choose "Library Maintenance", then "Check library", then "Yes" when calibre asks if you want it to check if the files in your library match the database. Calibre will then show you all "books" in your library that it does not have in its database.
If there are lots of "extra books" then you need to look for why. The most common reasons are:
- Having your library on a network drive (you seem to be doing this).
- Having your library in a folder synced to the cloud.
- Having some sync/backup program running.
- Aggressive antivirus.