How to make citation number start from the first Chapter instead of table of contents?

Question

I am writing my thesis work and I face an issue of citation numbering order. Some of my figures have citations in them which is why my citation numbering starts from List of Figures in table of content. Hence the Chapter 1 citations are starting from numbers 5 and onwards which is spoiling the whole citation format. The code is as follows:

% thesis.tex
%
%=====================================================================
% Document Style
%=====================================================================
% Choose only one of the following document classes:
%
% for a 12 Point NUST PhD Thesis without Margin Check
\documentclass[12pt]{nustthesis}
%
% for a 10 Point NUST PhD Thesis with Margin Check
%\documentclass[10pt,margincheck]{nustthesis}
%
% The margincheck option flags lines which overflow their hbox with a black
%  box at the end of the line.  This usually (but not always) indicates a
%  margin violation on the right margin.  Left margin violations aren't
%  indicated and if the margin violation is large enough, there isn't room
%  for the black box to be visiable.
%
% This option can be also used in conjunction with the msthesis option.
%
% or for a 12 Point NUST Masters Thesis
%\documentclass[12pt,msthesis]{nustthesis}
%
% or for a 10 Point NUST Masters Thesis
%\documentclass[10pt,msthesis]{nustthesis}
%
% The msthesis option changes the  margins from 1" all around
% (the PhD format) to 1.25" left and 1" remaining margins (MS format).
% The defaults for degree and thesis are changed to be MS and thesis.
% These defaults can be overridden if the margins for the MS thesis
% are desired for other documents.
% To include optional packages, use the \usepackage command.
%  The package epsfig is used to bring in the Encapsulated PostScript
%    figures into the document.
%  The package times is used to change the fonts to Times Roman; however
%    because the times typewriter font looks odd, the original LaTeX
%    Computer Modern font is kept for the typewriter font using
%      \renewcommand{\ttdefault}{cmtt}
%    Note that Times Roman is a PostScript font and therefore, the document
%    cannot be correctly viewed from the .dvi file.  It should be converted
%    to a .ps file first and then viewed with a PostScript previewer...
\usepackage{epsfig}
%\usepackage{lmodern}
\usepackage{times}
%\usepackage{fullpage,doublespace}
\usepackage{graphicx}
%\usepackage{color}
\usepackage{amsfonts}
\renewcommand{\ttdefault}{cmtt}
% This is for color online viewing version
\usepackage[pdftex,plainpages=false,pdfpagelabels,hypertexnames=false,colorlinks=true,backref,bookmarks=true,pdffitwindow=true,pdfstartview=FitH,pdfpagemode=UseOutlines]{hyperref}
% This is for Black and White printing version
%\usepackage[pdftex,plainpages=false,pdfpagelabels,hypertexnames=false,colorlinks=false,bookmarks=false,pdffitwindow=true,pdfstartview=FitH,pdfpagemode=UseOutlines]{hyperref}
\hypersetup{%
pdftitle = {Muhammad Danyal Khan MS Thesis}, pdfsubject = {Muhammad Danyal Khan's
MS Thesis}, pdfkeywords = {Speech Recognition, ASR, Call Center, audio transcription, Urdu language, Urdu ASR, Speech to Text, AI, Cyber Security}, pdfauthor = {\textcopyright

Muhammad Danyal Khan}, pdfcreator = {\LaTeX\ with package \flqq
hyperref\frqq}, pdfproducer =
{pdfeTeX-0.\the\pdftexversion\pdftexrevision} }
%\usepackage[chapter]{algorithm} (change by Arshad)
\usepackage{algorithm}
\usepackage{algorithmic}
%\usepackage[end]{algpseudocode}
\usepackage{makeidx}  % allows for indexgeneration
\DeclareGraphicsExtensions{.jpg, .pdf, .mps, .png}
\usepackage[title]{appendix}
\usepackage{longtable} %Arshad
\usepackage[table]{xcolor}
\usepackage{colortbl}
% \usepackage{color}
%\newcommand{\algorithmicrequire}{\textbf{Input:}}
%\newcommand{\algorithmicensure}{\textbf{Output:}}
%\newcommand{\algorithmicend}{\textbf{end}}
%\newcommand{\algorithmicif}{\textbf{if}}
\usepackage{acronym}
\newcommand{\acrolabel}[1]{\makebox[3cm][l]{\textbf{#1}}}
\newenvironment{acronyms}{\begin{list}{}{\renewcommand{\makelabel}{\acrolabel}}}{\end{list}}
\usepackage{tabu}
\usepackage{multirow}
\usepackage{tabularx}
\usepackage{adjustbox}
\usepackage{booktabs}% for better rules in the table
\usepackage{graphicx}
%\usepackage{subfigure}
%\usepackage{color}
%\usepackage{colortbl}
%\usepackage{soul}
\usepackage{pdflscape}
\usepackage{xltabular}
\usepackage{arabtex}
\usepackage{utf8}
\setcode{utf8}
% Essential packages
\usepackage{amsmath, amssymb, amsthm} % AMS Packages
%\usepackage{graphicx,color}           % Packages for graphics and color
\usepackage[left=1.5in, right=1in, top=1in, bottom=1in, includefoot, headheight=13.6pt]{geometry}
\DeclareMathOperator*{\argmax}{argmax} % thin space, limits underneath in displays
% Optional customization packages
\usepackage{lmodern}                  % Custom fonts
\usepackage[T1]{fontenc}              % Ensure correct font encoding
\usepackage{url}
\usepackage{enumitem}
\usepackage{pdflscape}
\usepackage{listings}
\lstloadlanguages{C,Java,XML,html,python,bash}
%Code listing style named "mycoding"
\lstdefinestyle{mycoding}{
  backgroundcolor=\color{lightgray}, commentstyle=\color{green},
  keywordstyle=\color{magenta},
  numberstyle=\tiny\color{darkgray},
  stringstyle=\color{purple},
  basicstyle=\ttfamily\footnotesize,
  breakatwhitespace=false,

  breaklines=true,

  captionpos=b,

  keepspaces=true,

  numbers=left,

  numbersep=5pt,

  showspaces=false,

  showstringspaces=false,
  showtabs=false,

  tabsize=2
}
\renewcommand{\lstlistingname}{Code}% Listing -> Code %% to change Code caption
\renewcommand{\lstlistlistingname}{List of \lstlistingname s}% List of Listings -> List of Codes
%\usepackage{./styles/astron}
%\usepackage{xspace}
%\usepackage[leqno]{amsmath}
%\usepackage{hyperref}
%\usepackage{sfmath}
%\usepackage{setspace} 
\usepackage{./styles/nust}
\title{AUTOMATIC SPEECH AND SENTIMENT RECOGNITION TO IDENTIFY MALICIOUS ACTIVITY/ MAL-INTENDED SPEECH}
%\subtitle{A sub-title}
\author{MUHAMMAD DANYAL KHAN}
\regno{00000359178}
\degree{\Master of Science in Cyber Security} % MSCSE, MSCCS
\school{Pakistan Navy Engineering College}
\adviser{Professor Dr Arshad Aziz }
\adviserAffiliation{Department of Cyber Security }
\graphicspath{{./img/}{./figs/}}
% Section symbol
%\usepackage{cleveref}
%\crefname{section}{\S}{\S\S}
%\Crefname{section}{\S}{\S\S}
%\crefname{subsection}{\S}{\S\S}
%\Crefname{subsection}{\S}{\S\S}
%========================================================================
%  Draft Control Commands:
%========================================================================
%
% \psdraft causes the \psfig or \epsfig commands to draw a box and label
% the box with the postscript file name instead of reading in the full
% postscript figure.  This can save time and toner when printing drafts.
%
%\psdraft
%
%
% \psfull causes the inclusion of the postscript figures.
%\psfull
%
%
%\pagestyle{thesisdraft} causes the footer text to become:
% DRAFT: Do Not Distribute        <time><Date>        <input file name>
%
%\pagestyle{thesisdraft}
%
%\pagestyle{thesis} causes the header and footers to be the correct format
%
\pagestyle{thesis}
%
%
%  The page margins can be marked with a post-script box using the
%  \draftmargins command.  This command uses dvips's end-of-page hook
%  This is only visible in the .ps file (NOT the .dvi file)!
%
%\draftmargins
%
%
%  The word ``DRAFT'' can be diagonally printed across the page using
%  the \draftscreen command.  This command uses dvip's beginning-of-page
%  hook.  This is only visible in the .ps file (NOT the .dvi file)!
%
%\draftscreen
%=======================================================================
% Remove the following lines if appendix tables or figures are present.
% The suppress writing the auxiliary information which appears in the
% list of tables or list of figures.
%
%\noappendixtables                % Don't have appendix tables
%\noappendixfigures               % Don't have appendix figures
%\renewcommand{\appendixname}{Appendix}
%\def@chapapp{Appendix}
%\def\appendixname{Appendix}
%=======================================================================
% End of Preamble, start of document
%
\begin{document}
% Choose your bibliography style
% plain is the basic style, others include ieeetr, siam, asm, etc
%\bibliographystyle{ieeetr}
\appendixname{Appendix}
\include{coverpage}
\include{prelude}                % Title page, abstract, table of contents, etc
\include{chapters/chapter1}
\include{chapters/chapter2}
\include{chapters/chapter3}
\include{chapters/chapter4}
\include{chapters/chapter5}
\include{chapters/chapter6}
\include{chapters/chapter7}

\bibliography{references.bib}
%\bibliography{refs}              % Make the bibliography
\bibliographystyle{ieeetr}
%\nocite{*}
\clearpage \pagenumbering{roman}  % This makes the page numbers Roman (i, ii, etc)
%\newpage
\begin{appendices}               % Start of the Appendix
\appendixtitleon
\appendixname
\appendixname{Appendix}
\renewcommand{\appendixname}{Appendix}
\def@chapapp{Appendix}
\renewcommand@chapapp{Appendix}
\def\chaptername{Appendix}
\def\appendixname{Appendix}
\def\appendixname{Appendix}\chaptername{Appendix}
%Chapters.  If there is only
                %one Appendix Chapter, then use \begin{appendix}
%\begin{appendix}
\appendix
\include{appendix1}
%\include{appendix2}
%\include{appendix3}
%\include{appendix4}





%\end{appendix}
\end{appendices} % End of the Appendix Chapters.
%\include{vita}   % Optional Vita, use \begin{vita} vita text \end{vita}
\end{document}```
How do we set the numbering of citation to begin from my Chapter 1 instead of Table of Contents List of Figures.