\documentclass{standalone}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage{pgfplotstable}

% Uncomment to make second error bar disappear
\pgfplotsset{compat=1.9}

\begin{document}

\pgfplotstableread{
xpos firsty secondy yerrdown yerrup
1           0         1                0.1               0.1
2           1         0               1.5               0.4
3           2         1               0.3               0.4
}\dataTable

\begin{tikzpicture}
\pgfplotsset{set layers}
\begin{axis}[
ybar stacked
    ]
% Layers needed to get error bars on top of lower blue rectangle
\addplot table[on layer=axis grid,x=xpos, y=firsty]{\dataTable};
\addplot+[mark=*,on layer=axis lines,error bars/.cd, y dir=both, y explicit] table[x=xpos, y=secondy, y error minus=yerrdown, y error plus=yerrup]{\dataTable};

\end{axis}

\end{tikzpicture}


\end{document}
