I found some older remarks regarding this, but think will create a bug report for future record:
\begin{dot2tex}[dot]
digraph G {
compound=true;
subgraph cluster_one {
a;
}
subgraph cluster_two {
b;
}
a -> b [ltail=cluster_one lhead=cluster_two];
}
\end{dot2tex}
This currently doesn't generate edge between two clusters, instead it generates edge between a and b