This is a sample code I used to counter the problem.
\begin{frame}{Topic 1}
Topic of the figures
\begin{figure}
\captionsetup[subfloat]{position=top,labelformat=empty}
\only<1>{\subfloat[Fig. 1]{\includegraphics{figure1.jpg}}}
\only<2>{\subfloat[Fig. 2]{\includegraphics{figure2.jpg}}}
\only<3>{\subfloat[Fig. 3]{\includegraphics{figure3.jpg}}}
\end{figure}
\end{frame}