\documentclass{article}
\usepackage{amsmath,amssymb,amsthm}
\usepackage{catchfilebetweentags}
\usepackage{todonotes}
\begin{document}
\section{Catch Method}
\label{sec:catch-method}

New test \todo{\ExecuteMetaData[external-fixmes.tex]{1}}
Some text 
\section{New section}
\label{sec:new-section}
Now we observe \todo{\ExecuteMetaData[external-fixmes.tex]{2}}
\end{document}