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After compiling the nomenclature I started noticing against my citations in the bibliography. For example:

A. Ahmed, Y. Low, M. Aly, V. Josifovski, and A. J. Smola. Scalable distributed infer-
ence of dynamic user interests for behavioral targeting. In SIGKDD, 2011. 5.2

where the 5.2 is the chapter it was referenced. This wasn't there before I ran the nomencl command:

makeindex thesis.nlo -s nomencl.ist -o thesis.nls

I'm not entirely sure why the nomenclature affects the bibliography and would like to remove this.

Incase I've done something stupid I included my preamble below:

\documentclass[12pt,a4paper,twoside,british]{report}
\usepackage{newtxmath}
\usepackage{newtxtext}
\usepackage{bm}
\usepackage[]{fontenc}
\usepackage[latin1,utf8]{inputenc}
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{3}
\usepackage[authoryear]{natbib}


\makeatletter
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{url}
\usepackage{refstyle}
\usepackage{caption}
\usepackage{subcaption}
\usepackage[titletoc]{appendix}
\usepackage{chngcntr}
\usepackage{algpseudocode}
\usepackage[]{algorithm2e}
\usepackage[acronym]{glossaries}
\usepackage{nomencl}
\makenomenclature


\usepackage{suthesis-2e}
\usepackage{graphicx}        
\usepackage{array}         % another package for table
\usepackage{color}
\definecolor{navy}{rgb}{0, 0, 0.5}
\usepackage[
  backref,
  bookmarks,
  pdfstartview=FitH,
  bookmarksopen=true,
  plainpages=false,
  colorlinks=true,
  urlcolor=navy,
  citecolor=black,
  linkcolor=black,
  pdftitle={DOCUMENT TITLE},
  pdfauthor={YOUR NAME},
  pdfpagelabels,
  bookmarksnumbered=true]{hyperref}
\usepackage{cleveref} 
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So turns out it was due to the order in which I placed hyperref and nomencl packages. For future reference make sure that hyperref appears before nomencl and glossaries package as below:

\usepackage{hyperref}
\usepackage{glossaries}
\usepackage{nomencl}

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