I don't think there is any minipage package, but the minipage environment is defined in the LaTeX kernel, so no packages are required to use it. The code you show doesn't work because you've used \caption outside a floating environment (figure), it has nothing to with the minipage or operating system.
So you could add a figure environment around the two minipages to allow the use of \caption. You would need to remove the \\ in the caption, as that doesn't work, but using an empty line instead works fine. You could also use the technique described in Line break in table caption using beamer.
However, you could also just ditch the caption altogether. Remove \caption from your code and it compiles fine.
You could also use the columns and column environments provided by beamer. As noted by Ignasi in a comment, if you add onlytextwidth as an option to the columns, i.e. \begin{columns}[onlytextwidth], the extra space seen in the last frame below won't be added, giving a result similar to that in the third frame.
The code below illustrates all these approaches. The demo option causes the images to be replaced by black rectangles, so you don't want that for your real document.

\documentclass[demo]{beamer}
\begin{document}
\begin{frame}
\frametitle{Original code without caption}
\begin{minipage}{.5\textwidth}
\hspace{-1.25cm}
\centering
\includegraphics[height=0.55\textheight]{figA.pdf}\\
\hspace{-1.25cm}
caption of figA\\
\scriptsize\textcolor{red}{[Wu et al., Nature (2009)]}
\end{minipage}%
\begin{minipage}{.5\textwidth}
\hspace{+0.25cm}
\centering
\includegraphics[height=0.55\textheight]{figB.pdf}\\
\hspace{+0.25cm}
caption of figB\\
\scriptsize\textcolor{red}{[Tizio, Caio et al., Nature (2006)]}
\end{minipage}
\end{frame}
\begin{frame}
\frametitle{With figure environment}
\begin{figure}
\begin{minipage}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figA.pdf}
\caption{caption of figA
\scriptsize\textcolor{red}{[Wu et al., Nature (2009)]}}
\end{minipage}%
\begin{minipage}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figB.pdf}
\caption{caption of figB
\scriptsize\textcolor{red}{[Tizio, Caio et al., Nature (2006)]}}
\end{minipage}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Modified version with just minipages}
\begin{minipage}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figA.pdf}
caption of figA
\scriptsize\textcolor{red}{[Wu et al., Nature (2009)]}
\end{minipage}%
\begin{minipage}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figB.pdf}
caption of figB
\scriptsize\textcolor{red}{[Tizio, Caio et al., Nature (2006)]}
\end{minipage}
\end{frame}
\begin{frame}
\frametitle{columns example}
\begin{columns}
\begin{column}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figA.pdf}
caption of figA
\scriptsize\textcolor{red}{[Wu et al., Nature (2009)]}
\end{column}%
\begin{column}{.5\textwidth}
\centering
\includegraphics[height=0.55\textheight]{figB.pdf}
caption of figB
\scriptsize\textcolor{red}{[Tizio, Caio et al., Nature (2006)]}
\end{column}
\end{columns}
\end{frame}
\end{document}
minipageenvironment is defined by the LaTeX kernel I believe, you don't need any package to use it. Edit: Andgenmpageshould be part of MacTeX I think, so you shouldn't need to install it. – Torbjørn T. Apr 07 '14 at 04:21\begin{minipage}{5cm}...\end{minipage}. The error you get from that code iscaption outside float, which makes sense as there is nofigureenvironment. However, you don't really need\captionhere do you? If you remove just\captionyour code works fine. – Torbjørn T. Apr 07 '14 at 05:12