I often encounter undesirable transformation of formulae I type in Mathematica. For text and formulae I use cells with Text style.
Say, I try to enter the formula
Something similar happens to me if I write, for example, Subscript[x, 1] (in 2-dimensional notation) in an input cell, then select the expression, and finally choose the menu Insert > Typesetting > Start inline cell. What I get literally looks like this:
\!\(
\*SuperscriptBox[\(x\), \(2\)]\)
Likewise with Superscript. However, I think this is not a natural sequence of operations.