That can happen when the DB does not match the BOOK folders.
That kind of corruption happen when most of the things listed by others were done.
The DB
MUST remain in lockstep with the folders. CaLIBRE MUST BE THE ONLY THING THAT MAKES CHANGES.
ANYTHING that breaks that, leads to the results you see.
In the case of those 'No Book with ID..." you just remove the entry since it does not point to a book (folder)
Was the a case in the report where there were
similar books found but no DB entry . That could be from a rename that was done by something NOT Calibre.