Problem with the subscripts of adjacent sums

This can be solved using the mathtools package and its command \adjustlimits:

\documentclass{article}
\usepackage{mathtools}
\begin{document}
\[
  \adjustlimits\sum_{i \in X}\sum_{i \in \bar{X}}
\]
\end{document}

Vertical adjustments are also possible via \vphantom:

\documentclass{article}
\begin{document}
\[
  \sum_{i \in X}\sum_{i \in \bar{X}} \quad \mbox{compared to} \quad
  \sum_{i \in X\vphantom{\bar{X}}}\sum_{i \in \bar{X}}
\]
\end{document}\end{document}​