(Note: See EDIT below that rules out both stackengine and standalone as the culprit)
Input:
\documentclass{standalone}
\usepackage{unicode-math}
\usepackage{stackengine}\stackMath
\begin{document}
\(\bigl[
,
\mathchoice%
{}%
{}%
{}%
{\stackunder{\scriptscriptstyle a}{}}
\bigr]\)
\end{document}
We expect the output [,] with same-size vertically aligned brackets. However, the output is as follows:
The brackets have different sizes and irregular vertical placement, which is wrong: they should have the same size and be vertically aligned. Using \Big, \bigg, etc. instead of \big produces similarly erroneous output.
Removing \usepackage{unicode-math}, or, \scriptscriptsize, or, a, or \stackunder doesn't trigger the bug any more.
The compilation was done with the following software versions:
- XeTeX, Version 3.14159265-2.6-0.99996 (TeX Live 2016/Debian) (preloaded format=xelatex 2017.4.2)
- LaTeX2e <2017/01/01> patch level 3
- standalone 2015/07/15 v1.2 (NOT responsible)
- unicode-math 2015/09/24 v0.8c
- stackengine 2016/10/04 v4.00 (NOT responsible)
Who is the culprit and what to do?
EDIT by S.B. Segletes
The stackengine package is shown not to be the culprit, by the following MWE, which produces the identical wrong result without the use of stackengine. Changing standalone to article also does not correct the issue.
\documentclass{standalone}
\usepackage{unicode-math}
\begin{document}
\(\bigl[
,
\mathchoice%
{}%
{}%
{}%
{\hbox{$\scriptscriptstyle a$}}
\bigr]\)
\end{document}



stackengineas the culprit. – Steven B. Segletes Jun 19 '17 at 15:19unicode-mathfrom my MWE fixes the issue... – Steven B. Segletes Jun 19 '17 at 16:36