I think it's time we ALL learn a bit about the PDF files we are all so obviously using!
In *every* PDF file there is a "title". In (nearly) *every* application that creates a PDF file you can set the "title" of the PDF file. For MAC, this is true for "File->Print -- Save As PDF" and "File->Export as PDF" which covers all the APPLE software, and nearly all non Apple MAC software.
With the latest version of iBooks (1.5), Apple evidently decided that it was a GOOD idea to show the user (that's us) the "title"s WE PUT IN OUR PDF FILES! If the titles of your PDF files are wrong, confusing, or just plain unwanted, then FIX or REMOVE them. Correcting bad or misleading DATA is always preferable to ignoring or hiding it - just because you don't see it doesn't mean it isn't bad - and someone else *will* see it, sometime!
Preview (MAC) shows you the TITLE in the inspector window, so you can see what the title of the PDF file is, even when it doesn't match the file name in the file system. I, personally, think showing the TITLE is a GOOD THING, and should be kept. If Apple goofed anywhere, it was in NOT giving us (their loyal users) a setting in iBooks that would allow us to turn OFF the display of TITLES and use FILE NAMES instead.
How do you change it or remove a title? The options are *way* too numerous to list. If you're totally lost, ask a knowledgeable friend for help, or go to the originator of the PDF file, Adobe, and buy their PDF editor (Acrobat). Also, there are plenty of other editors out there, if you don't like Acrobat.