Try the following
\documentclass[11pt]{article}
\usepackage[fleqn]{amsmath}
\begin{document}
\newcounter{eqnthing}\setcounter{eqnthing}{0}
\[a+b=c\refstepcounter{eqnthing}\label{maththing}\]
\par See(\ref{maththing}).
\refstepcounter{eqnthing}\label{linething}
\par See (\ref{linething}).
\end{document}
The first reference will not work. Then comment out \usepackage[fleqn]{amsmath} and it will work. It also works with \usepackage{amsmath} so the fleqn option appears to be the culprit.
Is this a known bug? Is there a workaround?



\labelwhen using[fleqn]inamsmath. It may work well with\tag, but what if you want to do something else? Not being able to imagine that other things might be feasible or even desirable doesn't make it okay to break existing functionality. – Geoff Pointer Nov 04 '14 at 14:06