The Journal of Web Engineering's LaTeX code completely redefines the sectional units in such a way that referencing them is not possible using the default \label-\ref system. Here's a view on what the sectioning commands look like:
%--------------------------------------------------------------------------
% section commands
\newcounter{sectionc}\newcounter{subsectionc}\newcounter{subsubsectionc}
\renewcommand{\section}[1] {\vspace{12pt}\addtocounter{sectionc}{1}
\setcounter{subsectionc}{0}\setcounter{subsubsectionc}{0}\noindent
{\bf\thesectionc. #1}\par\vspace{5pt}}
\renewcommand{\subsection}[1] {\vspace{12pt}\addtocounter{subsectionc}{1}
\setcounter{subsubsectionc}{0}\noindent
{\bf\thesectionc.\thesubsectionc. {\kern1pt \bfit #1}}\par\vspace{5pt}}
\renewcommand{\subsubsection}[1] {\vspace{12pt}\addtocounter{subsubsectionc}{1}
\noindent{\rm\thesectionc.\thesubsectionc.\thesubsubsectionc.
{\kern1pt \it #1}}\par\vspace{5pt}}
\newcommand{\nonumsection}[1] {\vspace{12pt}\noindent{\bf #1}
\par\vspace{5pt}}
Not only do they use old font declarations, there's no proper \refstepcounter to capture \labels. Instead, the package uses \addtocounter{<cntr>}{1}. For starters, you'd have to redefine \section to use \refstepcounter instead of \addtocounter. However, since this is for a journal submission, you should really question whether this is intended.
Here's a proper redefinition of \section included in a minimal example:

\documentclass{article}
\usepackage{jwe}
\makeatletter
\@addtoreset{subsectionc}{sectionc}
\@addtoreset{subsubsectionc}{subsectionc}
\makeatother
\renewcommand{\section}[1]{%
\par\vspace{12pt}%
\refstepcounter{sectionc}% This allows you to use \label and \ref properly
\noindent{\bfseries\thesectionc. #1}%
\par\vspace{5pt}}
\begin{document}
\section{Intro}\label{s1}
\noindent I am a boy.
\section{Two}
\noindent Related Works referring to Section~\ref{s1}.
\end{document}
My thought on this is that the journal probably wants people to do these references manually, which seems awkward.
Contact the journal and tell them they need to change things. Or at least ask them why they do it this way.
\documentclassare you using? In fact, we should be able to replicate your current problem in order to help you. For this, please construct a minimal working example (MWE). – Werner Aug 24 '15 at 17:08\section{Intro} \label{s1} \noindent I am a boy.
\section{Two} \noindent Related Works referring to Section~\ref{s1}.
\end{document}
– Aug 25 '15 at 10:11jwe.sty? – Werner Aug 25 '15 at 15:00