I have some long equations to deal with that don't fit into one line, and love the multlined-environment from mathtools to fit them into (e.g.) an align-environment, particularly if I want to package 2-3 manipulations of the quantity requiring two lines into one block (in the MWE there's only one for brevity).
However, multlined breaks down when there's a \substack inside, see MWE below. It seems that the environment somehow tries to "multline" the \substack, but I haven't managed to prevent multline from "seeing" the \substack to avoid this.
MWE (using knowledge from https://tex.stackexchange.com/a/180549/42225 and the documentation):
\documentclass[12pt,fleqn]{article}
\usepackage{amsmath}
\usepackage{mathtools}
\begin{document}
\noindent A long equation using \texttt{multline} and \texttt{$\backslash$substack},
%
\begin{multline*}
\mathcal{X}=\sum_{\substack{i,j,k,\ell,m,n,p,q,r,s,t\\ i+j\equiv 1 \bmod{2}}} \binom{...}{i} \binom{...}{j} \binom{...}{k} \binom{...}{\ell} \binom{...}{m} \binom{...}{n} \cdot\ldots\\
\ldots \cdot \binom{...}{p} \binom{...}{q} \binom{...}{r} \binom{...}{s} \binom{...}{t},
\end{multline*}
%
breaks when using \texttt{multlined} instead of \texttt{multline},
%
\begin{align*}
\MoveEqLeft[2]% default is 2em
\mathcal{X}\\
&\!\begin{multlined}[t][\linewidth-\mathindent-2em-\multlinegap]
=\sum_{\substack{i,j,k,\ell,m,n,p,q,r,s,t\\ i+j\equiv 1 \bmod{2}}} \binom{...}{i} \binom{...}{j} \binom{...}{k} \binom{...}{\ell} \binom{...}{m} \binom{...}{n} \cdot\ldots\\
\ldots \cdot \binom{...}{p} \binom{...}{q} \binom{...}{r} \binom{...}{s} \binom{...}{t},
\end{multlined}\\
&=1,
\end{align*}
%
but still works fine without \texttt{$\backslash$substack},
%
\begin{align*}
\MoveEqLeft[2]% default is 2em
\mathcal{X}\\
&\!\begin{multlined}[t][\linewidth-\mathindent-2em-\multlinegap]
=\sum_{i,j,k,\ell,m,n,p,q,r,s,t} \binom{...}{i} \binom{...}{j} \binom{...}{k} \binom{...}{\ell} \binom{...}{m} \binom{...}{n} \cdot\ldots\\
\ldots \cdot \binom{...}{p} \binom{...}{q} \binom{...}{r} \binom{...}{s} \binom{...}{t}.
\end{multlined}\\
&=1,
\end{align*}
\end{document}

amsmathormathtools; in either case, i'm adding it to theamsmathbugs list, as this is a reasonable construction that should be able to work without problems. – barbara beeton Oct 03 '15 at 14:51multlineddoes behind the scenes. – daleif Oct 05 '15 at 09:14