I changed my main font to "Times New Roman" and I have the same problem, so I don't think that the problem is the "Myriad Pro" font that I use.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The Legrand Orange Book
% Structural Definitions File
% Version 2.0 (9/2/15)
%
% Original author:
% Mathias Legrand (legrand.mathias@gmail.com) with modifications by:
% Vel (vel@latextemplates.com)
%
% This file has been downloaded from:
% http://www.LaTeXTemplates.com
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------------------------------------------------------------------------------
% VARIOUS REQUIRED PACKAGES AND CONFIGURATIONS
%----------------------------------------------------------------------------------------
\usepackage[table]{xcolor}
\usepackage[top=2.5cm,bottom=2.5cm,inner=3cm,outer=2cm,headsep=10pt,a4paper]{geometry} % Page margins
\linespread{1.1}
\usepackage{graphicx} % Required for including pictures
\graphicspath{{Pictures/}} % Specifies the directory where pictures are stored
\usepackage{lipsum} % Inserts dummy text
\usepackage{tikz} % Required for drawing custom shapes
\usepackage[english]{babel} % English language/hyphenation
\usepackage{enumitem} % Customize lists
\setlist{nolistsep} % Reduce spacing between bullet points and numbered lists
\usepackage{booktabs} % Required for nicer horizontal rules in tables
\usepackage{xcolor} % Required for specifying colors by name
\definecolor{ocre}{RGB}{243,102,25} % Define the orange color used for highlighting throughout the book
\usepackage{array}
\usepackage[version=4]{mhchem}
\usepackage{tcolorbox}
\usepackage[version=4]{mhchem}
\mhchemoptions{textfontcommand=\sffamily}
\mhchemoptions{mathfontcommand=\mathsf}
\usetikzlibrary{positioning,shapes.callouts}
%----------------------------------------------------------------------------------------
% FONTS
%----------------------------------------------------------------------------------------
\usepackage{avant} % Use the Avantgarde font for headings
\usepackage{times} % Use the Times font for headings
\usepackage{mathptmx} % Use the Adobe Times Roman as the default text font together with math symbols from the Symbol, Chancery and Computer Modern fonts
\usepackage{microtype} % Slightly tweak font spacing for aesthetics
\usepackage[utf8]{inputenc} % Required for including letters with accents
\usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs
\usepackage{fontspec}
\usepackage{titlesec}
\defaultfontfeatures{Ligatures=TeX}
\setsansfont{Times New Roman}
\setmainfont{Myriad Pro}
%----------------------------------------------------------------------------------------
% BIBLIOGRAPHY AND INDEX
%----------------------------------------------------------------------------------------
\usepackage[style=numeric,citestyle=numeric,sorting=nyt,sortcites=true,autopunct=true,babel=hyphen,hyperref=true,abbreviate=false,backref=true,backend=biber]{biblatex}
\addbibresource{bibliography.bib} % BibTeX bibliography file
\defbibheading{bibempty}{}
\usepackage{calc} % For simpler calculation - used for spacing the index letter headings correctly
\usepackage{makeidx} % Required to make an index
\makeindex % Tells LaTeX to create the files required for indexing
%----------------------------------------------------------------------------------------
% THEOREM STYLES
%----------------------------------------------------------------------------------------
\usepackage{amsmath,amsfonts,amssymb,amsthm} % For math equations, theorems, symbols, etc
\newcommand{\intoo}[2]{\mathopen{]}#1\,;#2\mathclose{[}}
\newcommand{\ud}{\mathop{\mathrm{{}d}}\mathopen{}}
\newcommand{\intff}[2]{\mathopen{[}#1\,;#2\mathclose{]}}
\newtheorem{notation}{Notation}[chapter]
% Boxed/framed environments
\newtheoremstyle{ocrenumbox}% % Theorem style name
{0pt}% Space above
{0pt}% Space below
{\normalfont}% % Body font
{}% Indent amount
{\small\bf\sffamily\color{ocre}}% % Theorem head font
{\;}% Punctuation after theorem head
{0.25em}% Space after theorem head
{\large\sffamily\color{lightblue4}\thmname{#1}\nobreakspace\thmnumber{\@ifnotempty{#1}{}\@upn{#2}}% Theorem text (e.g. Theorem 2.1)
\thmnote{\nobreakspace\the\thm@notefont\sffamily\bfseries\color{black}---\nobreakspace#3.}} % Optional theorem note
\renewcommand{\qedsymbol}{$\blacksquare$}% Optional qed square
\newtheoremstyle{blacknumex}% Theorem style name
{5pt}% Space above
{5pt}% Space below
{\normalfont}% Body font
{} % Indent amount
{\small\bf\sffamily}% Theorem head font
{\;}% Punctuation after theorem head
{0.25em}% Space after theorem head
{\small\sffamily{\tiny\ensuremath{\blacksquare}}\nobreakspace\thmname{#1}\nobreakspace\thmnumber{\@ifnotempty{#1}{}\@upn{#2}}% Theorem text (e.g. Theorem 2.1)
\thmnote{\nobreakspace\the\thm@notefont\sffamily\bfseries---\nobreakspace#3.}}% Optional theorem note
\newtheoremstyle{blacknumbox} % Theorem style name
{0pt}% Space above
{0pt}% Space below
{\normalfont}% Body font
{}% Indent amount
{\small\bf\sffamily}% Theorem head font
{\;}% Punctuation after theorem head
{0.25em}% Space after theorem head
{\small\sffamily\thmname{#1}\nobreakspace\thmnumber{\@ifnotempty{#1}{}\@upn{#2}}% Theorem text (e.g. Theorem 2.1)
\thmnote{\nobreakspace\the\thm@notefont\sffamily\bfseries---\nobreakspace#3.}}% Optional theorem note
% Non-boxed/non-framed environments
\newtheoremstyle{ocrenum}% % Theorem style name
{5pt}% Space above
{5pt}% Space below
{\normalfont}% % Body font
{}% Indent amount
{\small\bf\sffamily\color{ocre}}% % Theorem head font
{\;}% Punctuation after theorem head
{0.25em}% Space after theorem head
{\small\sffamily\color{ocre}\thmname{#1}\nobreakspace\thmnumber{\@ifnotempty{#1}{}\@upn{#2}}% Theorem text (e.g. Theorem 2.1)
\thmnote{\nobreakspace\the\thm@notefont\sffamily\bfseries\color{black}---\nobreakspace#3.}} % Optional theorem note
\renewcommand{\qedsymbol}{$\blacksquare$}% Optional qed square
\makeatother
% Defines the theorem text style for each type of theorem to one of the three styles above
\newcounter{dummy}
\numberwithin{dummy}{section}
\theoremstyle{ocrenumbox}
\newtheorem{theoremeT}[dummy]{Theorem}
\newtheorem{problem}{Problem}[chapter]
\newtheorem{exerciseT}{}[chapter]
\theoremstyle{blacknumex}
\newtheorem{exampleT}{Example}[chapter]
\theoremstyle{blacknumbox}
\newtheorem{vocabulary}{Vocabulary}[chapter]
\newtheorem{definitionT}{Definition}[section]
\newtheorem{corollaryT}[dummy]{Corollary}
\theoremstyle{ocrenum}
\newtheorem{proposition}[dummy]{Proposition}
%----------------------------------------------------------------------------------------
% DEFINITION OF COLORED BOXES
%----------------------------------------------------------------------------------------
\RequirePackage[framemethod=default]{mdframed} % Required for creating the theorem, definition, exercise and corollary boxes
% Theorem box
\newmdenv[skipabove=7pt,
skipbelow=7pt,
backgroundcolor=black!5,
linecolor=ocre,
innerleftmargin=5pt,
innerrightmargin=5pt,
innertopmargin=5pt,
leftmargin=0cm,
rightmargin=0cm,
innerbottommargin=5pt]{tBox}
% Exercise box
\newmdenv[skipabove=7pt,
skipbelow=7pt,
rightline=false,
leftline=true,
topline=false,
bottomline=false,
%backgroundcolor=lightblue4!10,
%linecolor=lightblue4,
innerleftmargin=5pt,
innerrightmargin=5pt,
innertopmargin=5pt,
innerbottommargin=5pt,
leftmargin=0cm,
rightmargin=0cm,
linewidth=0pt]{eBox} % Ήταν linewidth=4pt]{eBox}
% Definition box
\newmdenv[skipabove=7pt,
skipbelow=7pt,
rightline=false,
leftline=true,
topline=false,
bottomline=false,
linecolor=ocre,
innerleftmargin=5pt,
innerrightmargin=5pt,
innertopmargin=0pt,
leftmargin=0cm,
rightmargin=0cm,
linewidth=4pt,
innerbottommargin=0pt]{dBox}
% Corollary box
\newmdenv[skipabove=7pt,
skipbelow=7pt,
rightline=false,
leftline=true,
topline=false,
bottomline=false,
linecolor=gray,
backgroundcolor=black!5,
innerleftmargin=5pt,
innerrightmargin=5pt,
innertopmargin=5pt,
leftmargin=0cm,
rightmargin=0cm,
linewidth=4pt,
innerbottommargin=5pt]{cBox}
% Creates an environment for each type of theorem and assigns it a theorem text style from the "Theorem Styles" section above and a colored box from above
\newenvironment{theorem}{\begin{tBox}\begin{theoremeT}}{\end{theoremeT}\end{tBox}}
\newenvironment{exercise}{\begin{eBox}\begin{exerciseT}}{\end{exerciseT}\end{eBox}}
\newenvironment{definition}{\begin{dBox}\begin{definitionT}}{\end{definitionT}\end{dBox}}
\newenvironment{example}{\begin{exampleT}}{\hfill{\tiny\ensuremath{\blacksquare}}\end{exampleT}}
\newenvironment{corollary}{\begin{cBox}\begin{corollaryT}}{\end{corollaryT}\end{cBox}}