When typesetting the following MWE with xelatex I obtain an unexpected symbol, an empty square, between the two lines in the equation. It typesets fine in lualatex. The unexpected symbol shows up when using a different font for the text in math mode than for the other symbols, which is a fairly common thing to do. Similar problems have been reported before, such as here: Incompatibility with mathtools and unicode-math in xelatex?
However, the new example does not involved mathtools in any way.
The problem only shows up with certain font sets, as indicated in the MWE, below.
\documentclass{article}
\usepackage{amsmath}
\usepackage{fontspec}
\usepackage{unicode-math}
\setmathfont{xits-math.otf}
\setmathfont[range=up/{latin,Latin,num}]{XCharter-Roman.otf} % extra character appears between two lines
%\setmathfont[range=up/{latin,Latin,num}]{Charis SIL} % extra character appears between two lines
%\setmathfont[range=up/{latin,Latin,num}]{texgyretermes-regular.otf} % works okay with this
%\setmathfont[range=up/{latin,Latin,num}]{Times} % works okay with this
\begin{document}
\begin{equation*}
x = \begin{cases}
y \\ y
\end{cases}
\end{equation*}
\end{document}
Unless I am doing something wrong (always the most likely thing), I guess this is a bug, but I am not sure where - unicode-math, xelatex, the opentype font itself? Is it the same bug as has been reported before?

unicode-mathversion 0.8j, released 2018-01-07. – egreg Jan 10 '18 at 12:00