You can define subfigures:

\begin{pandoccrossrefsubfigures}

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

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

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

\caption{Caption}\label{fig:subfigures}

\end{pandoccrossrefsubfigures}

\begin{pandoccrossrefsubfigures}

\subfloat[1]{\pandocbounded{\includegraphics[keepaspectratio,alt={1}]{fig1.png}}\label{fig:subfig21}}

\subfloat[2]{\pandocbounded{\includegraphics[keepaspectratio,alt={2}]{fig2.png}}\label{fig:subfig22}}

\subfloat[3]{\pandocbounded{\includegraphics[keepaspectratio,alt={3}]{fig3.png}}}

\subfloat[4]{\pandocbounded{\includegraphics[keepaspectratio,alt={4}]{fig4.png}}\label{fig:subfig24}}

\subfloat[5]{\pandocbounded{\includegraphics[keepaspectratio,alt={5}]{fig5.png}}}

\subfloat[6]{\pandocbounded{\includegraphics[keepaspectratio,alt={6}]{fig6.png}}\label{fig:subfig26}}

\subfloat[7]{\pandocbounded{\includegraphics[keepaspectratio,alt={7}]{fig7.png}}\label{fig:subfig27}}

\subfloat[8]{\pandocbounded{\includegraphics[keepaspectratio,alt={8}]{fig8.png}}}

\subfloat[9]{\pandocbounded{\includegraphics[keepaspectratio,alt={9}]{fig9.png}}\label{fig:subfig29}}

\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}
