Other things being equal, TeX will aim to position subscripts and superscripts in places that “look good”. Unfortunately, it only does this for the sub- and superscripts of each atom at a time, so if you have

the second subscript will appear higher, since the first has moved down to avoid the superscript; the effect can be noticeably distracting:$ X^{1}_{2} X_{2} $

You can avoid the problem, for a single instance, by

here, the dummy superscript has the requisite “pushing down” effect:$ X^{1}_{2} X^{}_{2} $

While this technique does what is necessary, it is tedious and
potentially error-prone. So, for more than one or two equations
in a document, the LaTeX user is advised to use the
*subdepth* package, which forces the lower position for all
subscripts.

- subdepth.sty
- subdepth

This question on the Web: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=subheight