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
$ X^{1}_{2} X_{2} $
the second subscript will appear higher, since the first has moved
down to avoid the superscript;
the effect can be noticeably distracting:
You can avoid the problem, for a single instance, by
$ X^{1}_{2} X^{}_{2} $
here, the dummy superscript has the requisite “pushing down” effect:
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.
This question on the Web: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=subheight
