You can define subfigures:

\begin{pandoccrossrefsubfigures}

\subfloat[1]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig1.png}\label{fig:subfig1}}
\subfloat[2]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig2.png}\label{fig:subfig2}}
\subfloat[3]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig3.png}}

\subfloat[4]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig4.png}\label{fig:subfig4}}
\subfloat[5]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig5.png}}
\subfloat[6]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig6.png}\label{fig:subfig6}}

\subfloat[7]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig7.png}\label{fig:subfig7}}
\subfloat[8]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig8.png}}
\subfloat[9]{\includegraphics[width=0.3\textwidth,height=\textheight]{fig9.png}\label{fig:subfig9}}

\caption[{Caption}]{Caption}

\label{fig:subfigures}

\end{pandoccrossrefsubfigures}

\begin{pandoccrossrefsubfigures}

\subfloat[1]{\includegraphics{fig1.png}\label{fig:subfig21}}

\subfloat[2]{\includegraphics{fig2.png}\label{fig:subfig22}}

\subfloat[3]{\includegraphics{fig3.png}}

\subfloat[4]{\includegraphics{fig4.png}\label{fig:subfig24}}

\subfloat[5]{\includegraphics{fig5.png}}

\subfloat[6]{\includegraphics{fig6.png}\label{fig:subfig26}}

\subfloat[7]{\includegraphics{fig7.png}\label{fig:subfig27}}

\subfloat[8]{\includegraphics{fig8.png}}

\subfloat[9]{\includegraphics{fig9.png}\label{fig:subfig29}}

\caption[{Caption}]{Caption}

\label{fig:subfigures2}

\end{pandoccrossrefsubfigures}

Figures themselves can be referenced fig.~\ref{fig:subfigures2}, as well
as individual subfigures:
figs.~\ref{fig:subfig1}, \ref{fig:subfig2}, \ref{fig:subfig29}
