Here is my MWE

\documentclass[letterpaper]{article}%
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{breqn}
\begin{document}
\begin{dmath}
q^{\prime}\left(  t\right)   =\operatorname{Re}\left(  i\omega_{n}\left(q_{0}-i\frac{q_{0}^{\prime}}{\omega_{n}}\right)  e^{i\omega_{n}t}\right)
                             =\operatorname{Re}\left(  \left(  \omega_{n}q_{0}-e^{i\frac{\pi}{2}}%q_{0}^{\prime}\right)  e^{i\frac{\pi}{2}}e^{i\omega_{n}t}\right)
                             =\operatorname{Re}\left(  \left(  \omega_{n}q_{0}e^{i\frac{\pi}{2}}-e^{i\pi}q_{0}^{\prime}\r…

This is the original MWE, which compiles OK

\documentclass[letterpaper]{article}%
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}

\begin{document}

\begin{align*}
q^{\prime}\left(  t\right)   &  =\operatorname{Re}\left(  i\omega_{n}\left(
q_{0}-i\frac{q_{0}^{\prime}}{\omega_{n}}\right)  e^{i\omega_{n}t}\right) \\
&  =\operatorname{Re}\left(  \left(  \omega_{n}q_{0}-e^{i\frac{\pi}{2}}%
q_{0}^{\prime}\right)  e^{i\frac{\pi}{2}}e^{i\omega_{n}t}\right) \\
&  =\operatorname{Re}\left(  \left(  \omega_{n}q_{0}e^{i\frac{\pi}{2}}%

I was wondering what might cause \raggedbottom not do its job?

\documentclass[letterpaper]{article}%
\input{commonlatex}
\raggedbottom

I use

\documentclass[letterpaper]{article}%
\raggedbottom
\begin{document}
\begin{multicols}{2}
\tableofcontents
.....
\end{multicols}
\end{document}

\documentclass[demo]{article}
\RequirePackage[demo]{graphicx}
\usepackage[nopar,numbers]{kantlipsum}
\usepackage[left=.7in,right=.5in,top=.7in,bottom=.9in]{geometry}
\usepackage{multicol}
\raggedbottom
\begin{document}
\begin{multicols}{2}
\section{one}
\kant[1-5]
\section{two}
\includegraphics[width=8cm,height=10cm]%
\kant[1-4]

\end{multicols}
\end{document}

\documentclass[demo]{article}
\RequirePackage[demo]{graphicx}
\usepackage[numbers]{kantlipsum}
\usepackage[left=.7in,right=.5in,top=.7in,bottom=.9in]{geometry}
\usepackage{multicol}
\raggedbottom
\begin{document}
\begin{multicols}{2}
\section{one}
\kant[1-5]
\section{two}
\includegraphics[width=8cm,height=10cm]%
\kant[1-4]

\end{multicols}
\end{document}

This is even better example:
\documentclass[demo]{article}
\RequirePackage[demo]{graphicx}
\usepackage[numbers]{kantlipsum}
\usepackage[left=.7in,right=.5in,top=.7in,bottom=.9in]{geometry}
\usepackage{multicol}
\raggedbottom
\begin{document}
\begin{multicols}{2}
\section{one}
\kant[1-5]
\section{two}
This is start of section two.

\includegraphics[width=8cm,height=10cm]%
\kant[1-4]

\end{multicols}
\end{document}

Example again, has small thing not right. But still show the problem.
\documentclass[demo]{article}
\RequirePackage[demo]{graphicx}
\usepackage[numbers]{kantlipsum}
\usepackage[left=.7in,right=.5in,top=.7in,bottom=.9in]{geometry}
\usepackage{multicol}
\raggedbottom
\begin{document}
\begin{multicols}{2}
\section{one}
\kant[1-5]
\section{two}
This is start of section two.

\includegraphics[width=8cm,height=10cm]{}

\kant[1-4]

\end{multicols}
\end{document}

\raggedbottom
\raggedcolumns % !!!!!

@DavidCarlisle, you are right, just tried it with
\section{...}
\begin{figure}
\includegraphics[scale=0.6]{problem_3_description_small.png}%
\end{figure}

and without using \ragged anything. and now the problem went away. But the figure went very far away from where I wanted to be. So floating figures do not really do it. I like the \raggedcolumn more, since now the image is where I want it and also no stretch

\begin{document}

\mbox{\ldboxbrace {abc}{abc}\rdboxbrace {abc}{abc}}

\end{document}

Overfull \hbox (21.12148pt too wide) in paragraph at lines 46--47

}
}

\documentclass{article}
\usepackage[utf8]{inputenc}


\usepackage[hyperindex=true]{hyperref}
\usepackage{imakeidx}
\makeindex[program=texindy,options=-M mystyle.xdy]
%\makeindex

\usepackage{filecontents}
\begin{filecontents*}{mystyle.xdy}
;;; xindy style file
(markup-locclass-list :open "\dotfill" :sep "")

(define-attributes (( "textbf" "default" )) )
(markup-locref   :attr  "textbf"     :open "\textbf{\hyperpage{" :close "}}")
(markup-locref   :attr  "textit"     :open "\textit{\hyperpage{" :close "}}")

!config
# requires arara 3.0+
identifier: clean
name: NewCleaningTool
commands:
- <arara> COMMAND HERE @{wait}
- <arara> @{remove}
arguments:
- identifier: remove
  default: <arara> @{isFalse(file == getOriginalFile(), isWindows("cmd /c del", "rm -f").concat(' "').concat(file).concat('"'))}
- identifier: wait
  flag: <arara> @{parameters.wait}
  default: 5

- <arara> powershell -command "Start-Sleep -s @{wait}"