\documentclass[12pt]{report}
\usepackage{amsfonts,amsmath,mathtools}
\begin{document}
\begin{align*}
0\longrightarrow S
\xrightarrow{
\begin{array}{c}
xyz\\
\end{array}
\left[\begin{array}{rrr}
1 \\-1 \\1 \\
\end{array}
\right]
\begin{matrix}
\\yz\\xz\\xy
\end{matrix}
}S^3
\xrightarrow{
\begin{array}{rrr}
yz&xz&xy\\
\left[\begin{array}{rrr}
0&1&1\\
1&0&-1\\
-1&-1&0\\
\end{array}
\right]
\end{array}
}S^3
\end{align*}
\end{document}
I want to align the row yz xz xy with the top row of the 3 by 3 matrix given in the code
\end{array}
missing. At least your code does not compile. Please try to give us compilable code and to give more information on what you want to achieve and what you have tried so far.