I have a few \cite commands in my pgfplots which are not being displayed properly when externalization in on. As soon as you turn off the externalization, the references will be displayed correctly.
\documentclass{article}
\usepackage{pgfplots}
\usepgfplotslibrary{external}
\tikzexternalize
\begin{document}
\begin{tikzpicture}
\begin{axis}[xmin=-1,xmax=1,xlabel = \cite{Lorem}, title=\cite{Lorem2}, ylabel=\cite{Lorem3}]
\addplot
coordinates{ (0,0)(2,2)};
\end{axis}
\end{tikzpicture}
\begin{thebibliography}{99\kern\bibindent}
\bibitem{Lorem}\textsc{Lorem ipsum dolor sit}
\texttt{Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras vitae purus mi. Fusce quam urna, elementum at ullamcorper in, tempus sed quam.}
\bibitem{Lorem2}\textsc{Lorem ipsum dolor sit}
\texttt{Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras vitae purus mi. Fusce quam urna, elementum at ullamcorper in, tempus sed quam.}
\bibitem{Lorem3}\textsc{Lorem ipsum dolor sit}
\texttt{Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras vitae purus mi. Fusce quam urna, elementum at ullamcorper in, tempus sed quam.}
\end{thebibliography}
\end{document}
