Package titlesec Warning: Non standard sectioning command \section

Question

I have a problem with a package that I am not aware I am using ... Here is my main.tex

\RequirePackage{silence}
\WarningFilter{remreset}{The remreset package} %s shut up about obsolete package
% book example for classicthesis.sty
\documentclass[
  % Replace twoside with oneside if you are printing your thesis on a single side
  % of the paper, or for viewing on screen.
  oneside,
  %twoside,
  11pt, a4paper,
  footinclude=true,
  headinclude=true,
  cleardoublepage=empty
]{scrbook}

\usepackage{lipsum}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{acronym}
\usepackage{listings} % ajouté pour corriger les deux erreurs de compilation
\usepackage{graphicx}
\usepackage{tabularx}
\usepackage[dvipsnames]{xcolor} 
\usepackage{pdfpages}
\usepackage{hyperref}
\usepackage{microtype}
\hypersetup{
    colorlinks=true,
    linkcolor=blue,
    filecolor=magenta,      
    urlcolor=NavyBlue,
    citecolor=NavyBlue,
}
\usepackage[english]{babel}
\usepackage[largesc]{newpxtext} 
\useosf
\linespread{1.05}
\usepackage[utf8]{inputenc}
%\usepackage{wrapfig}
\usepackage{rotating}
\usepackage{epigraph}
\tolerance=1
\emergencystretch=\maxdimen
\hyphenpenalty=10000
\hbadness=10000
\usepackage[font=small,skip=0pt]{caption}
\usepackage{listings}
\lstset{
  basicstyle=\ttfamily,
  columns=fullflexible,
  frame=single,
  breaklines=true,
  postbreak=\mbox{\textcolor{red}{$\hookrightarrow$}\space},
}
\usepackage{soul} %to allow highlighting text that requires attention
\newcommand{\hash}[1]{{\ttfamily\seqsplit{#1}}}
\begin{document}
\input{titlepage.tex}
\input{first.tex}
%\include{FrontBackMatter/abstract}
%\include{FrontBackMatter/dedication}
%\include{FrontBackMatter/acknowledgements}
%\include{FrontBackMatter/declaration}

\include{FrontBackMatter/contents}

\chapter{Introduction}
\input{chapter1.tex}

\chapter{Genome assembly}
\input{chapter2.tex}

\chapter{Mutation accumulation}
\input{chapter3.tex}

\chapter{Perspectives}
\input{chapter4.tex}
 
\chapter{Bibliography}    
\bibliographystyle{naturemag}
\bibliography{bibliography}  
\chapter{annexes - publications}
\input{annexes.tex}
\end{document}

The compilation returns

Package titlesec Warning: Non standard sectioning command \section detected. Using default spacing and no format.

What is that titlesec package? I am not loading it. I am just using \section and \subsection throughout the document.

Any idea?

Thanks a lot, that would be hugely appreciated.

EDIT: here is the miminal example

Package titlesec Warning: Non standard sectioning command \section detected. Using default spacing and no format.

Is this actually a harmless warning? Or does it run the risk to cause other problems?

\RequirePackage{silence}
\WarningFilter{remreset}{The remreset package} 
\documentclass[
  % Replace twoside with oneside if you are printing your thesis on a single side
  % of the paper, or for viewing on screen.
  oneside,
  %twoside,
  11pt, a4paper,
  footinclude=true,
  headinclude=true,
  cleardoublepage=empty
]{scrbook}

\usepackage{lipsum}
\usepackage[linedheaders,parts,pdfspacing]{classicthesis}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{acronym}
\usepackage{listings} 
\usepackage{graphicx}
\usepackage{tabularx}
\usepackage[dvipsnames]{xcolor} 
\usepackage{pdfpages}
\usepackage{hyperref}
\usepackage{microtype}
\hypersetup{
    colorlinks=true,
    linkcolor=blue,
    filecolor=magenta,      
    urlcolor=NavyBlue,
    citecolor=NavyBlue,
}
\usepackage[english]{babel}
\usepackage[largesc]{newpxtext} 
\useosf
\linespread{1.05}
\usepackage[utf8]{inputenc}
%\usepackage{wrapfig}
\usepackage{rotating}
\usepackage{epigraph}
\tolerance=1
\emergencystretch=\maxdimen
\hyphenpenalty=10000
\hbadness=10000
\usepackage[font=small,skip=0pt]{caption}
\usepackage{listings}
\lstset{
  basicstyle=\ttfamily,
  columns=fullflexible,
  frame=single,
  breaklines=true,
  postbreak=\mbox{\textcolor{red}{$\hookrightarrow$}\space},
}
\usepackage{soul} %to allow highlighting text that requires attention
\newcommand{\hash}[1]{{\ttfamily\seqsplit{#1}}}
\begin{document}

\chapter{Introduction}
\section{youpla boum}
blablabal 


\end{document}

Answer 1

classicthesis has some design flaws, especially using KOMA-Script and titlesec, which the author acknowledges in the package documentation (he is planning a e-design):

However, there are still many remains from older times in the code, many dirty workarounds here and there, and several other things I am absolutely not proud of (for example my unwise combination of KOMA and titlesec etc.).

The warning is just a warning, not an error. You can probably ignore it. But you might run into other problems in the future. So, if you have a choice, maybe consider using another document class...