I am using a template to write up a proposal. The only issue is when I try to have a table of Contents, it comes up numbered with a zero.

\documentclass{proposal}
\usepackage{epsfig}
\usepackage{fontspec}
\setsansfont{Roboto Condensed}
\usepackage{xcolor,lipsum}
\usepackage{titlesec}
\titleformat{name=\section}[block]
{\sffamily\large}
{}
{0pt}
{\colorsection}
\titlespacing*{\section}{0pt}{\baselineskip}{\baselineskip}
\usepackage[english]{babel}
\usepackage[utf8]{inputenc}
\usepackage{fancyhdr}

\pagestyle{fancy}
\fancyhf{}

\newcommand{\colorsection}[1]{%
\colorbox{blue!20}{\parbox{\dimexpr\textwidth-2\fboxsep}{\thesection\ #1}}}

\begin{document}
\begin{titlepage}
\begin{center}
\vspace*{1cm}

\Huge
\textbf{Research Proposal}

\vspace{1cm}
\LARGE
Project: ?

\vspace{2.5cm}

\textbf{Bla bla }

\vspace{6cm}

James Bond

\vspace{0.8cm}

\Large  A research initiative in collaboration with the .... \\

\end{center}

\end{titlepage}

\newpage

\tableofcontents

\newpage

\section{Preliminary title}

Text ....

\section{Scientific Interest}

More text.

\section{Main Research Question(s)}

More text.  Cite an example \cite[]{sample_ref}

\section{Originality}

\section{Research Methodology}

\section{Viability}

\section{Practical Relevance}

\section{Work Plan for Three Years}
\subsection{First Year}
\subsection{Second Year}
\subsection{Third Year}
\section{Education of the PhD Candidate}
\bibliography{•}

\newpage
\end{document}

• Welcome to TeX.SX! You can have a look at our starter guide to familiarize yourself further with our format. – Johannes_B Apr 21 '14 at 11:24
• Your titleformat calls colorsection in which the numbering is defined. – Johannes_B Apr 21 '14 at 11:32

The problem is that \colorsection always typesets the value for the counter; one way to prevent this is to use two \titleformats one for the numbered sections and another one with the numberless option to typeset the title for unnumbered sections; the decision is made using a conditional; something along these lines:

\documentclass{article}
\usepackage{xcolor}
\usepackage{titlesec}

\newif\ifnumbered
\titleformat{name=\section}[block]
{\sffamily\large\numberedtrue}
{}
{0pt}
{\colorsection}
\titleformat{name=\section,numberless}[block]
{\sffamily\large\numberedfalse}
{}
{0pt}
{\colorsection}
\titlespacing*{\section}{0pt}{\baselineskip}{\baselineskip}

\newcommand{\colorsection}[1]{%
\colorbox{blue!20}{\parbox{\dimexpr\textwidth-2\fboxsep}{\ifnumbered\thesection\ \relax\fi#1}}}

\begin{document}

\tableofcontents
\section{Test numbered section}
\section*{Test unnumbered section}
\section{Another test numbered section}

\end{document}


With the current definition of \colorsection, the presence/absence of descendants in the title might produce inconsistent heights for the color boxes; adding \struts might prevent this:

\newcommand{\colorsection}[1]{%
\colorbox{blue!20}{\parbox{\dimexpr\textwidth-2\fboxsep}{\ifnumbered\thesection\ \relax\fi\strut#1\strut}}}


I suppressed from my example code all information from the original question that was not relevant to the issued at hand and changed to the article document class, since I don't have proposal; the solution, however, should work with the original settings.