Compliments, you have found a little bug of the package.
As David has already said, you can safely ignore it.
However, the package allows you to set the width of the missing figure. If you like, you may use this option to avoid the warning.
I've added \usepackage{showframe}
only to show how the figure goes out of the margin. Obviously, don't add it to your document unless you need it for debugging purposes.
Moreover, I'd suggest to you to add \setlength{\marginparwidth}{2.9cm}
otherwise the margin todo notes are too narrow.
\documentclass[12pt,a4paper]{report}
\usepackage[left=3.5cm,right=3.5cm,top=3cm,bottom=3cm]{geometry}
\usepackage[utf8]{inputenc}
\setlength{\marginparwidth}{2.9cm}% a suggestion
\usepackage[colorinlistoftodos, textwidth=\marginparwidth]{todonotes}
\usepackage{showframe}% only for testing purpose
\begin{document}
Bla.
\missingfigure{This figure the original figure which causes the warning.}
\missingfigure[figwidth=\textwidth-2pt]{This is the figure with corrected width and no errors.}
More bla.
I suggest also to increase the \verb|\marginparwidth|.
\todo{test todo note}
\end{document}
EDIT: If you have a lot of \missingfigure
and don't like to put [figwidth=\textwidth-2pt]
every time, you may add \renewcommand
in your preamble:
\usepackage[colorinlistoftodos, textwidth=\marginparwidth]{todonotes}
\let\oldmissingfigure\missingfigure% save old command
\renewcommand{\missingfigure}[1]{\oldmissingfigure[figwidth=\textwidth-2pt]{#1}}% renew \missingfigure command
or, alternatively, if you need to use [figwidth=...]
in some cases, you may create a \newcommand
and use one or the other according to your needs:
\documentclass[12pt,a4paper]{report}
\usepackage[left=3.5cm,right=3.5cm,top=3cm,bottom=3cm]{geometry}
\usepackage[utf8]{inputenc}
\usepackage{makecell}
\setlength{\marginparwidth}{2.9cm}% a suggestion
\usepackage[colorinlistoftodos, textwidth=\marginparwidth]{todonotes}
\newcommand{\missingfig}[1]{\missingfigure[figwidth=\textwidth-2pt]{#1}}% new \missingfigure command
\usepackage{showframe}% only for testing purpose
\begin{document}
Bla.
\missingfig{This figure is missing with new command}
More bla.
\missingfigure[figwidth=0.5\textwidth]{This figure is missing half textwidth}
\end{document}