Well, I do not know class mnras and I do not have a documentation of it. You gave no link to the class, but I guess you mean this one?.
If you have a look into the file mnras.cls you can find in the definition of command \maketitle in the line 1058: \let\thanks\relax. That means that this class does not allows command \thanks in the title.
The class you use is very restricted and I suggest to use a standard class, if you have not to submit an paper with that class.
Anyway, if you use this class you should take a look into the example file and follow the coments (saying: do not change this lines. That means too: Do not delete this lines).
The following MWE compiles with 4 warnings (two because the footnotes, two because the class has to be maintained):
\documentclass{mnras}%
\usepackage[T1]{fontenc}
\usepackage[english]{babel}
\usepackage{blindtext}
\begin{document}
\label{firstpage} % <===================================================
\pagerange{\pageref{firstpage}--\pageref{lastpage}}% <==================
\title[short title]{Title}
\author[K. T. Smith et al.]{
Keith T. Smith,$^{1}$\thanks{E-mail: mn@ras.org.uk (KTS)}
A. N. Other,$^{2}$\thanks{E-mail: Joe@doe.org}
Third Author$^{2,3}$
and Fourth Author$^{3}$
\\
% List of institutions
$^{1}$Royal Astronomical Society, Burlington House, Piccadilly, London W1J 0BQ, UK\\
$^{2}$Department, Institution, Street Address, City Postal Code, Country\\
$^{3}$Another Department, Different Institution, Street Address, City Postal Code, Country
}
%\date{Accepted XXX. Received YYY; in original form ZZZ}
%
%\pubyear{2015}
\maketitle
%\begin{abstract}
%\blindtext
%\end{abstract}
\begin{keywords} % commenting results in missing thanks notes!
keyword1 -- keyword2 -- keyword3
\end{keywords}
\section{Section 1}
This is Text with a footnote\footnote{This is a footnote}
\Blindtext
\Blinddocument
% <============================================ Don't change these lines
%\bsp % typesetting comment
\label{lastpage}
\end{document}
I added the parts you have deleted (see markings < ======= in the code) and tested a little bit. Theese tests showed me, that you are allowed to omit the abstract, but not the keywords. Comment the environment keywords and recompile. The \thanksfootnotes disapear. And the class does not want footnotes in the title.
The result of the MWE above is:

The class gives in the header the first and last line (see first red marking). Thats the reason why you are not allowed to delete/change the lines you did.
The other red markings shows the footnotes and their footnotemarks in text and title.
I suggest you call or contact the maintainer of this class or the journal asking you to use this class if you need to use it for your paper. Report the errors/problems you have and ask for a correction of the class ...
\end{document}. Then we can copy and compile and test your code ... – Mensch Oct 26 '15 at 02:45