The problem here is that arrayjob does some nasty stuff to get the value out of the array and this is not compatible with how \includegraphics handles its arguments.

There are two solutions:

1. expand and then use

\documentclass[class=minimal,border=0pt,tikz]{standalone}
\usepackage{tikz}
\usepackage{arrayjob}

\begin{document}

    \newarray\ggg
    \readarray{ggg}{64&61&41}
    \ggg(1)

    \foreach \subfig in {1,2,3}
    {
        %This is Figure \subfig
        \checkggg(\subfig)
        \includegraphics[page=\cachedata]{mysubfigures};
    }
\end{document}

Here \checkARRAYNAME(INDEX) will save the value in the macro \cachedata so we can use it in the arguments normally since that will not need special treatment to rewrite to the value.

2. use pgfmath's arrays

Since you are using tikz the package pgfmath is already loaded and it is able to understand arrays. Simply do:

\def\ggg{{64,61,41}} % <- your array is just a list    

    \foreach \i in {0,1,2} % 0-based indexes
    {
        %This is Figure \i
        \pgfmathsetmacro{\pg}{\ggg[\i]} % <- array notation ARRAY[INDEX]
        \includegraphics[page=\pg]{mysubfigures}
    }

A third way

Unless you really need arrays somewhere else in your document, you do not need them here as you can just exploit the excellent \foreach syntax:

\foreach[count=\i] \pg in {64,61,41} {
    Subfigure~\i, Page~\pg:
    \includegraphics[page=\pg]{mysubfigures}
}