Problem with how Bibliography appears

Question

I have a Bibliography.bib file with the following code:

@online{Bacterial_Classification,
  author   = "Franklin D. Lowy",
  title    = "Bacterial Classification, Structure and Function",
  url      = "https://api.semanticscholar.org/CorpusID:49963607",
  year     = 2008,
  note     = "Accessed: Columbia University",
  keywords = "Basics of Bacteria"
}
@article{Mass_Spectrometry,
  author =       "Anja Freiwald
and Sascha Sauer",
  title =        "Phylogenetic classification and identification of bacteria by mass spectrometry",
  journal =      "Nat Protoc",
  volume =       "4",
  number =       "5",
  pages =        "732-742",
  year =         "2009, doi: https://doi.org/10.1038/nprot.2009.37",
  DOI =          "https://doi.org/10.1038/nprot.2009.37",
  keywords =     "Spectrometry"
}

I have my main.tex file with the following:

\documentclass[twoside, a4paper, 11pt]{article}
\usepackage[figuresright]{rotating}
\renewcommand{\baselinestretch}{1.2}
\usepackage[top=2.5cm, left=2.5cm, right=2.5cm, bottom=2.5cm, headheight=1.25cm, footskip=1.25cm, margin=1in]{geometry}
\usepackage{tabularx}
\usepackage{array}
\usepackage{caption}
\captionsetup[figure]{name=Figure}
\captionsetup[table]{name=Table}
\usepackage{longtable}
\usepackage{ragged2e}
\justifying
\usepackage{fontspec}
\setmainfont{Times New Roman}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{afterpage}
\usepackage{esint}
\usepackage{listings}
\usepackage{color}
\usepackage{tcolorbox}
\usepackage{changepage}
\usepackage{subcaption}
\usepackage{setspace}
\usepackage{url}
\usepackage{multirow}
\usepackage{minted}
\setlength{\parindent}{0em}
\usepackage{float}
\usepackage{titlesec}
\titleformat{\section}
{\normalfont\LARGE\bfseries}{Chapter~\thesection :}{1em}{}
\usepackage{cite} 
\usepackage{xurl}
\bibliographystyle{IEEEtran}
\usepackage{hyperref}
\hypersetup{
    colorlinks=true,
    linkcolor=black,
    citecolor=black,
    filecolor=black,

    urlcolor=black,
    pdftitle={Comparative Study of Electronic Circuits for Bacterial Identification},
    pdfauthor={Dimitrios D. Koliouskas},
    pdfpagemode=FullScreen,
    }
\urlstyle{same}
\begin{document}
\section{Example}
\input{Chapter 1}
\clearpage
\pagestyle{plain}
\nocite{*}
\renewcommand{\refname}{REFERENCES}
\addcontentsline{toc}{section}{REFERENCES}
\bibliography{Bibliography}
\clearpage
\end{document}

I also have a Chapter 1.tex file with the following example code:

\subsection{Also an example}
Typing...
\cite{Bacterial_Classification}
\subsubsection{example no.2}
Typing...
\cite{Mass_Spectrometry}

With THIS specific example in a new blank project it works as it should. BUT in my real document it does not work and my 2nd cited paper (Mass_Spectrometry) appears first in references, with the number [1], instead of second, although I mentioned first the Bacterial_Identification. I must clarify that in my real document I really do not have anything else from packages to anything. Literally the only thing that changes is the text in the document and the number of .tex files. I really do not know where the problem is.

I JUST figured that any bibliography that I cite in the following will go first in references (This is an edit and I did not include the packages for figures/tables in my main.tex):

\begin{figure}[hbt]
\center
\resizebox{1\textwidth}{!}{\includegraphics{A bacterial sample to a protein extraction and the final analysis by mass spectrometry.jpg}}
\caption{A bacterial sample subjected to a protein extraction and the final analysis by mass spectrometry. \cite{Mass_Spectrometry}}
  \label{Fig:Mass Spectrometry}
\end{figure}

why is this happening? The funny thing is that the \cite{Bacterial_Classification} is mentioned 4 times before the above figure (1 inside the text and 3 in 3 different figures, all before the above-mentioned figure).