See this MWE:

\documentclass[full]{l3doc}

\title{An \pkg{l3doc} bug}
\author{Joel C. Salomon}

\begin{document}
\maketitle

\begin{documentation}

\begin{function}{\some_function_with_a_very_long_name:nnnnn}
  \begin{syntax}
    "\some_function_with_a_very_long_name:nnnnn" <first argument>
<second argument> <third argument> <fourth argument> <fifth argument>
    "\some_function_with_a_very_long_name:nnnnn"
      <first argument> <second argument> <third argument> <fourth argument>
      <fifth argument>
    "\some_function_with_a_very_long_name:nnnnn" %
       <first argument> <second argument> <third argument> <fourth
argument> %
       <fifth argument>
  \end{syntax}
  Notice how the first line is very very long in the source,
  but when I split it up, the split is reflected in the output.
  Adding comments just makes things worse.
\end{function}
\end{documentation}

\end{document}