Vertically aligning images in beamer

Using floating environments (such as figure or table) in a frame does not work in the way it should. To accomplish your objective, turn on allowpagebreak and T. Adjust the graphics with height option. See the code below for the remaining.

\documentclass{beamer}
\usepackage{graphicx}
\begin{document}
\frame[allowpagebreak,T]
{%
        \only<1>
        {%
            \centering
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-a}

            \vfill
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-a}
        }%

        \only<2>
        {%
            \centering
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-b}

            \vfill
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-b}
        }%

        \only<3>
        {%
            \centering
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-c}

            \vfill
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image-c}
        }%

        \only<4>
        {%
            \centering
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image}

            \vfill
            \includegraphics[height=\dimexpr0.5\textheight-0.5in]{example-image}
        }%
}
\end{document}

For creating GIF animation see my other answer here.

Instead of \vspace, you can use \\ to force a line break.

\documentclass{beamer}
\begin{document}
\frame{
    \begin{figure}[t!]
    \includegraphics<1>[scale=.5]{img} \\
    \includegraphics<1>[scale=.5]{img}

    \includegraphics<2>[scale=.5]{img} \\
    \includegraphics<2>[scale=.5]{img} 

    \includegraphics<3>[scale=.5]{img} \\
    \includegraphics<3>[scale=.5]{img}

    \includegraphics<4>[scale=.5]{img} \\
    \includegraphics<4>[scale=.5]{img} 

      \end{figure} 
    }   
\end{document}

If you only have one line break in total instead of one for every image pair, your problem should disappear. The point is that your \vspace{.1in} commanded is not masked by the <1>,<2>,<3>, or <4>:

\documentclass{beamer}
\begin{document}
\frame{
  \begin{figure}[t!]
    \includegraphics<1>[scale=.5]{fig/imageA1}
    \includegraphics<2>[scale=.5]{fig/imageA2}
    \includegraphics<3>[scale=.5]{fig/imageA3}
    \includegraphics<4>[scale=.5]{fig/imageA4}
    \vspace{.1in}        
    \includegraphics<1>[scale=.5]{fig/imageB1}
    \includegraphics<2>[scale=.5]{fig/imageB2}
    \includegraphics<3>[scale=.5]{fig/imageB3}
    \includegraphics<4>[scale=.5]{fig/imageB4}
  \end{figure} 
}   
\end{document}