I had the same problem in my document (and sadly also cannot upload a MWE) and "solved" it as suggested by Salivan in a comment:
Change the spacing a little
Even though it is not a real solution, but only fights the symptoms, it was the only way I could get a correct PDF.
In my case it was enough to replace : (colon, space) by :\ (colon, backslash, space) in the document, which changes the spacing only very little.
Details
For anyone interested in the problem, I put my preamble here. I removed all lines, where I'm 100% sure, that they're not related to the problem, like \newcommand, \tikzstyle, ... .
Since the problem disappears with the slightest change, the preamble is still quite large.
As described in the preamble, commenting out the line \newcounter{unusedCounter} "resolves" the problem. The counter is nowhere else used in the code.
The compilation log-file in the buggy case shows for the last counter of the bibtex-part:
\c@cbx@tempcntd=\count512
Maybe someone has an idea, whether this could mean something. I mean, a high powers of 2 that appears at the same time as a problem could very well be related to that problem. Still, I changed some other lines that led to a compilation where also \c@cbx@tempcntd=\count512, but the pdf-output was correct.
The preamble:
\documentclass[11pt, a4paper, twoside, cleardoublepage=plain, openright, hyphens]{scrbook}
\usepackage{etex}
\usepackage[utf8]{inputenc}
\usepackage[russian, ngerman, main=english, australian]{babel}
\usepackage[cmex10]{amsmath}
\usepackage{algcompatible}
\usepackage{algorithm}
\usepackage[noend]{algpseudocode}
\usepackage{subcaption}
\usepackage{amssymb}
\usepackage{blindtext}
\usepackage[usenames,dvipsnames]{xcolor}
\usepackage{tikz}
\usepackage[normalem]{ulem}
\usetikzlibrary{shapes,arrows,fit,calc}
\usetikzlibrary{arrows.meta}
\usetikzlibrary{backgrounds,calc,circuits.logic.US,positioning,intersections}
\usetikzlibrary{patterns, patterns.meta}
\usetikzlibrary{decorations.pathreplacing,angles,quotes}
\usetikzlibrary{shapes.geometric}
\usepackage{circuitikz}
\usepackage{graphicx}
\usepackage{makecell}
\usepackage{xspace}
\usepackage{arydshln}
\usepackage{mathtools}
\usepackage[usestackEOL]{stackengine}
\usepackage{scalerel}
\usepackage{titletoc}
\usepackage{enumerate}
\usepackage{lmodern}
\usepackage{bibentry}
\usepackage{multirow}
\usepackage{booktabs}
\usepackage[official]{eurosym}
\usepackage{amsthm}
\usepackage{soul}
\usepackage[most]{tcolorbox}
\usepackage[T1]{fontenc}
\usepackage{pifont}
\usepackage{pdftexcmds}
\usepackage{catchfile}
\usepackage{ifluatex}
\usepackage{ifplatform}
\usepackage{ifthen}
\usepackage{cancel}
\usepackage{microtype}
\usepackage{mathtools}
\usepackage{pdflscape}
\usepackage{enumitem}
\usepackage{filecontents}
\usepackage{etoolbox}
\usepackage{framed}
\usepackage{fancyhdr}
\usepackage{xpatch}
\newcommand{\pageeq}[2]{\ifthenelse{\pageref{#1}=\pageref{#2}}{p.~\pageref{#1}}{pp.~\pageref{#1}-\pageref{#2}}}
\newcommand{\Pageeq}[2]{\ifthenelse{\pageref{#1}=\pageref{#2}}{Page~\pageref{#1}}{Pages~\pageref{#1}-\pageref{#2}}}
\let\newclassictheorem\newtheorem
\let\classicproof\proof
\tcbset{
thmbox/.style={
enhanced,
breakable,
sharp corners=all,
fonttitle=\bfseries\normalsize,
fontupper=\normalsize\itshape,
top=0mm,
bottom=0mm,
right=0mm,
colback=white,
colframe=white,
colbacktitle=white,
coltitle=black,
attach boxed title to top left,
boxed title style={empty, size=minimal, bottom=1.5mm},
overlay unbroken ={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)|-%
(frame.south east)--(frame.north east);},
overlay first={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);
\draw (frame.north east)--(frame.south east);},
overlay middle={
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);
\draw (frame.north east)--(frame.south east);},
overlay last={
\draw ([xshift=3.5mm]frame.north west)|-%
(frame.south east)--(frame.north east);},
},
L/.style={thmbox,
overlay unbroken ={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)|-([xshift=15mm]frame.south west);},
overlay first={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);},
overlay middle={
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);},
overlay last={
\draw ([xshift=3.5mm]frame.north west)|-([xshift=15mm]frame.south west);},
},
LQ/.style={thmbox,
overlay unbroken ={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)|-([xshift=15mm]frame.south west);
\node[anchor=east] at (frame.south east) {$\square$};},
overlay first={
\draw (title.south west)--(title.south east);
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);},
overlay middle={
\draw ([xshift=3.5mm]frame.north west)--([xshift=3.5mm]frame.south west);},
overlay last={
\draw ([xshift=3.5mm]frame.north west)|-([xshift=15mm]frame.south west);
\node[anchor=east] at (frame.south east) {$\square$};},
},
}
\newcommand*\quotefont{\fontfamily{LinuxLibertineT-LF}}
\pagestyle{fancy}
\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
\fancyhead{}
\fancyhead[RO]{\slshape\nouppercase{\rightmark}}
\fancyhead[LE]{\slshape\nouppercase{\leftmark}}
\fancyfoot{}
\fancyfoot[LE,RO]{\thepage}
\newclassictheorem{hypothesis}[]{Hypothesis}
\newtcbtheorem[number within = section]{theobox}{Theorem}{thmbox,L,
before skip=1em plus 0.5em,
after skip=1em plus 0.5em}{thm}
\newtcbtheorem[use counter from=theobox]{defbox}{Definition}{thmbox,L, description delimiters parenthesis, separator sign none,
before skip=1em plus 0.5em,
after skip=1em plus 0.5em,
fontupper=\normalfont}{def}
%% Many more \newtcbtheorem[use counter from=theobox]
\newtcbtheorem[]{proofbox}{Proof}{thmbox,LQ,
before skip=1em plus 0.5em,
after skip=1em plus 0.5em}{proof}
\newcommand{\thmCounter}{tcb@cnt@theobox}
\newclassictheorem{algo}[\thmCounter]{Algorithm}
\newclassictheorem{algo-sketch}[\thmCounter]{Algorithm Sketch}
\makeatletter
\renewcommand\thealgorithm{\thesection.\arabic{\thmCounter}}
@addtoreset{algorithm}{\thmCounter}
\makeatother
%%%%%%%%%%%%%%%%% % Comment the following line out to dissolve problem
\newcounter{unusedCounter}
%%%%%%%%%%%%%%%%%
\usepackage[
backend=biber,
style=ieee,
sorting=nyt,
bibencoding=utf8,
defernumbers=true,
maxnames=10,
citestyle=numeric-comp
]{biblatex}
\assignrefcontextkeyws[labelprefix=J]{J}
\assignrefcontextkeyws[labelprefix=C]{C}
\assignrefcontextkeyws[labelprefix=B]{B}
\assignrefcontextkeyws[labelprefix=W]{W}
% Pseudo-Code
\makeatletter
\def\BState{\State\hskip-\ALG@thistlm}
\makeatother
% \hyphenation, \newcommand, \tikzstyle, ...
\usepackage[bookmarks=false]{hyperref}
pdflatex -vand see the result. Assuming it is found: Navigate to the folder containing your tex document. Then type:pdflatex yourfilename.texmodified for your file name. Works better if no spaces in file name. Does that compile as expected? If it does, then the problem is with WinEdit. But if you see the same problem, then the problem is with your TeX code. Note: Usexelatexorlualatexas compiler, if necessary. – Mar 20 '18 at 18:17pdflatex yourfilename.texrunbibtex yourfilenameand then againpdflatex yourfilename.textwice, so to have your references compiled. – Arzigoglu Mar 20 '18 at 19:48footmiscpackage with thehangoption interacting in some weird way with thehyperrefpackage. Any ideas or work-around that you found in the past 2 years? – user21820 Dec 10 '20 at 20:02hangoption fromfootmiscand replaced it with my own code:\makeatletter\renewcommand\@makefntext[1]{\setlength{\hangindent}{\footnotemargin}\noindent\rlap{\@makefnmark}\rule[0em]{\footnotemargin}{0em}#1}\makeatother. Do you remember whether you also used\footmiscwithhang? If so, then maybe this is the answer. – user21820 Dec 11 '20 at 04:59hangoption offootmisc. I am using thearticleclass with font size11, and found that changing\setlength\footnotemargin{1em}to\setlength\footnotemargin{11pt}resolved the bug, so I am very sure the bug is related to footnotes... – user21820 Jun 18 '21 at 09:33\setlength. Therefore, ironically, we can 'fix' the bug by just adding\newlength{\fixmissingtext}\setlength{\fixmissingtext}{1em}to the preamble!! – user21820 Feb 08 '22 at 12:35footmiscpackage. After all, I was only using thebottomandhangoptions. These can be imitated using theetoolboxpackage via\pretocmd{\footnoterule}{\vfill}{}{}and the code I provided above. Sigh. DIY seems best. – user21820 Mar 23 '22 at 18:50footmiscorfancyhdror any footnote-related package, the bug has returned. This is getting increasingly annoying as I have ≈ 200 pages and it is ridiculous if I have to check every single page every time I make a change... – user21820 Apr 05 '22 at 13:29