The following minimal code causes a small indentation at the beginning of the line of text, smaller than the usual indentation at the start of a paragraph. It disappears if the label in subequations is removed.
\documentclass{article}
\usepackage{mathtools}
\begin{document}
\begin{subequations}
\begin{gather}
a = b\\
b = c
\end{gather}
\label{eqn:test}
\end{subequations}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua \ref{eqn:test}.
\end{document}
I haven't noticed this effect in any other maths environments - is this a bug in subequations?
EDIT: replace gather* with gather