Appendix`s contents being shown under wrong heading in Table of Contents

Question

I am changing a pre-built template for my thesis. There is a main file named thesis.tex in which all the chapter files, references files and appendices files are included. The structure of this file is as follows

\include{chapter1}
\include{chapter2}
\include{chapter3}
\include{chapter4}
\include{chapter5}
\include{chapter6}
\include{chapter7}


% NEED TO CHANGE THE SECTION NUMBER FOR REFERENCES ACCORDINGLY
\addcontentsline{toc}{chapter}{8 \hskip 3.55em References}

\bibliographystyle{IEEEtran}  
\bibliography{references}

% COMMENT THE LINES ABOUT APPENDIX OUT IF YOU DO NOT HAVE THIS SECTION.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%                                                                 %
%                            APPENDICES                           %
%                                                                 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newpage\pagestyle{plain}
\theappendix

% NEED TO CHANGE THE SECTION NUMBER FOR REFERENCES ACCORDINGLY.
\addcontentsline{toc}{chapter}{9 \hskip 3.55em Appendices}

\include{appendix1}
%\include{appendix2}
\include{appendix3}

Problem:
The problem is with the appendices section. My first appedix contains some sections and figures. When i add this section to main file, the contents of this appendix are shown wrongly under other chapter in table of contents.

As you can see that the contents of Appendix are being shown under references chapter. I want them to be shown either under appendices section or completely hide them. What could be the possible solution?

Answer 1

An explanation of the behavior is eg in https://tex.stackexchange.com/a/386799. But the OP there uses a KOMA-Script class and its \addchaptertocentry command.

Suggestion: Replacing \include{appendix1} by \input{appendix1} should solve your issue.

---

If you really must use \include, then load package scrlfile and use:

\BeforeFile{appendix1.tex}{\addcontentsline{toc}{chapter}{9 \hskip 3.55em Appendices}}%  needs package scrlfile
\include{appendix1}

BTW: Your manual setting of the chapter number looks strange.