You will certainly have some \bibitem entries. If your bibliography is generated automatically, then the \bibitem commands will probably be in an automatically generated .bbl file with the same name (minus the extension) as your master (.tex) file.
If there are no blank lines after each \bibitem then adding them and running TeX ONCE should probably fix your problem, I think.
BibTeX, biblatex and biber ⇒ Citation links to bibliography at end
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