\documentclass{article}
\usepackage{amsmath}
\begin{document}

Issue 258:
\begin{align}
\begin{split}
x &= y \\
& z
\end{split} \label{eq:1} \\
\begin{split}
a &= b \\
& q
\end{split} \label{eq:2}
\end{align}

Issue 109:
\end{document}

