\RequirePackage[l2tabu,orthodox]{nag}
\documentclass{jsarticle}
\usepackage{amsmath}
\begin{document}
\footnote{
\begin{align}
x&\\y&
\end{align}
}
\end{document}
! Improper \halign inside $$'s.
<recently read> \halign
l.8 \end{align}
?
\everydisplay=\expandafter{\the\everydisplay \narrowbaselines}