\documentclass{article} 
\usepackage{filecontents}
\begin{filecontents}{\jobname.data.dat}
X	Y
1	3
2	7
3	4
\end{filecontents}

\begin{filecontents}{\jobname.error.dat}
Errors
1
3
5
\end{filecontents}

\usepackage{pgfplots,pgfplotstable}

\pgfplotstableread{\jobname.data.dat}\datatable

\pgfplotstableset{
	create on use/errors/.style={
		create col/copy column from table={\jobname.error.dat}{Errors}
	}
}


\begin{document}
\begin{tikzpicture}
\begin{axis}
% This doesn't work
%\tracingmacros=2 \tracingcommands=2
\addplot +[error bars/.cd, y explicit, y dir=both] table [y error=errors] {\jobname.data.dat};

% This works
%\addplot +[scatter] table [meta=errors] {data.dat};

\end{axis}
\end{tikzpicture}

\end{document}
