Comment 1 for bug 2023476

That indicates you somehow have hard links to the book file in your trash folder already.
You can simply empty the trash to fix the issue, but I would be
interested to know how the issue happened in the first place.

Did calibre crash during a previous delete attempt? Or is there
something unusual about the filesystem you have your calibre library on?
Can you come up with steps to reproduce the problem, after emptying the
trash folder?