Justification error in report format

Question

I am writing my thesis using Kile. I encountered a mis-justification problem when creating table of contents, please see the uploaded picture. My institute insists to fix this. Can anybody help me on this?

Here is my MWE:

\documentclass[12pt,a4paper]{report}
\usepackage{OkanFBEStyle}
\usepackage[pdftex]{graphicx}
\usepackage{subfigure}
\usepackage{boxedminipage}
\usepackage{enumerate}
\usepackage[nosort]{cite}
\usepackage{wrapfig}
\pdfminorversion=5
 \makeatletter
  \renewcommand{\thesubfigure}{\alph{subfigure}.\hskip-0.5\subfiglabelskip}
\renewcommand{\@@thesubfigure}{\thefigure.\alph{subfigure}}
  \makeatother
\usepackage{float}
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{array}
\usepackage{amssymb}
\usepackage{amsfonts}
\usepackage{amsmath}
\usepackage{amsxtra}
\usepackage{cases}
\usepackage{xfrac}
\setcounter{tocdepth}{3}
\usepackage{epstopdf}
\usepackage{pifont}
\usepackage{url}
\usepackage{hyperref}
\usepackage{color}
\usepackage{ctable}
\usepackage{tabularx}
\usepackage{soul}
\usepackage{lineno}
\usepackage{tikz}
\usetikzlibrary {calc}
\newcolumntype{x}[1]{
>{\raggedleft\hspace{0pt}}p{#1}}
\newcolumntype{+}{>{\global\let\currentrowstyle\relax}}
\newcolumntype{^}{>{\currentrowstyle}}
  \newcommand{\rowstyle}[1]{\gdef\currentrowstyle{#1}%
  #1\ignorespaces
  }
\newcommand{\otoprule}{\midrule[\heavyrulewidth]}
\newcolumntype{Z}{>{\centering\arraybackslash}X}

\begin{document}
\tableofcontents
\chapter{INTRODUCTION}
\section{Intramedullary Nailing}

\chapter{METHODS}
\section{Study 1: In modeling a distraction process, how should the tissue load be correctly represented in order to obtain a better understanding of the mechanical response of IM nails during limb lengthening?}
\subsection{Finite Element Model Considerations}
\end{document}

Answer 1

This is actually correct. The first line is indented and the other lines are not. Admitedly this looks akward. Consider using different headings in the text and in the table of contents.

Example:

\section[Study 1: Chairs]{Study 1: The behaviour of chairs in the wilderness under the influence of time, love and water -- considering different frequencies of quantim flux compensation during recomfubeling phase.}

Edit: As i understand the question it is about the alignment of the new lines in the section header with the indent of subsections. The fastest way to get rid of that problem is to not have linebreaks. You can introduce alternative header by giving them as an optional argument. The table of contents will show the alternative header. You can now write a shorter header that is suitable for a table of contents and still preserve the long header in the actual text.

Rereading your questions, you may have asked wheather it is possible to have the indent of 3.1 be equal to the indent of 3.1.X. If that is the case you want to take a look at the tocloft package. It allows you to configure the TOC.