This is a stream of counciousness post reply and I am just thinking how I might approach the problem you pose.
First – what output style are you using? Has it been edited to remove the “generic” template in the bibliography section and is this citation possibly a reference type that is unusual, and therefore isn’t included in your bibliography output style template. Using a different style which includes more templates (like APA 6th, or Harvard) might ‘reveal’ the missing one.
Or just try “Numbered” out of the box. Does it work to reveal the identity of the missing bibliography listing?
Finally, it is likely to be one of the citations listed as ‘1’ – under that list, unless it is used again in your manuscript? So again open them (using the edit reference) and check the reference type of each.