You may have a corrupt calibre library. The paths to the books have changed for some reason, most likely because of something you did. Possible causes might be that you have used some incompatible cloud service or copied the library between different operating systems or filesystems that are incompatible and cause minor changes to the paths.
I would recommend that you make a backup of the library and then try to run the library maintenence functions. With some luck calibre will be able to fix the problems for you.
http://manual.calibre-ebook.com/gui.html#library
Edit: What theducks said...