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}