Help with chapter bibliography and general bibliography in thesis

Question

I am submitting my PhD thesis and our department requires a separate bibliography for each chapter that contains an article, I have got 4 chapters, the first chapter is a literature review (not an article) which means I do not need to generate a bibliography for it. The university's template of the root file is as follows:

\documentclass[PhD,bibsection,english]{ulthese}
\ifxetex\else \usepackage[utf8]{inputenc} \fi
\titre{<Titre principal>}
\auteur{<Prénom Nom>}
  \direction{<Prénom Nom>, <directeur ou directrice> de recherche}
\begin{document}
\frontmatter
\frontispice
\include{resume}

\include{abstract}

\cleardoublepage
\tableofcontents

\cleardoublepage
\listoftables

\cleardoublepage
\listoffigures

\cleardoublepage
\dedicace{<Dédicace si désiré>}
\cleardoublepage
\epigraphe{<Texte de l'épigraphe>}{<Source ou auteur>}
\cleardoublepage
\include{remerciements}

\include{avantpropos}
\mainmatter
\include{introduction}

\include{chapitre1-articles}

\include{chapitre2-articles}

\include{conclusion}
\appendix
\include{annexe}
\end{document}

and they suggest having the following in each article chapter:

\bibliographystyle{plainnat}
\bibliography{references}

However, if I only use their code, I cannot generate the references of my first chapter (literature review), and I cannot generate the overall bibliography at the end of the document. If I add \bibliographystyle{plainnat} and \bibliography{references} to the root file as follows:

\documentclass[PhD,bibsection,english]{ulthese}
\ifxetex\else \usepackage[utf8]{inputenc} \fi
\bibliographystyle{plainnat}


\titre{<Titre principal>}
\auteur{<Prénom Nom>}
  \direction{<Prénom Nom>, <directeur ou directrice> de recherche}
\begin{document}
\frontmatter
\frontispice
\include{resume}

\include{abstract}

\cleardoublepage
\tableofcontents

\cleardoublepage
\listoftables

\cleardoublepage
\listoffigures

\cleardoublepage
\dedicace{<Dédicace si désiré>}
\cleardoublepage
\epigraphe{<Texte de l'épigraphe>}{<Source ou auteur>}
\cleardoublepage
\include{remerciements}

\include{avantpropos}
\mainmatter
\include{introduction}

\include{chapitre1-articles}

\include{chapitre2-articles}

\include{conclusion}
\appendix
\include{annexe}
\bibliography{references}
\end{document}

Then I try to do Bibtex, it shows the following error:

Illegal, another \bibstyle command---line 208 of file Chapter1.aux
 : \bibstyle
 :          {plainnat}
I'm skipping whatever remains of this command
Illegal, another \bibdata command---line 56 of file PhD_thesis_aziez_111187664.aux
 : \bibdata
 :         {references}
I'm skipping whatever remains of this command
Database file #1: references.bib
(There were 2 error messages)

In addition, the references in my first chapter (literature review) are all question marks "?", and the overall bibliography appears as a subsection of the conclusion as follows:

I tried some solutions including: chapterbib and bibunits but without any success. I hope that you can help me.