I think I've found a small bug in the way the showonlyrefs=true option in mathtools works. Consider this semi-minimal example:
\documentclass[12pt]{article}
\usepackage[utf8]{inputenc} % UFT8 - danske bogstaver og andet godt fra havet
\usepackage[T1]{fontenc}
\usepackage{siunitx}
\usepackage{amsmath}
\usepackage{mathtools}
\usepackage{mhchem}
\mathtoolsset{showonlyrefs=true} % ingen numerering af equations
\begin{document}
%
Seems fine
\begin{align*}
\Delta S &= \sum(S^{\ominus}(\text{produkter})) - \sum(S^{\ominus} (\text{reaktanter})) \\
\Delta S &= (\SI{214}{\joule\per\kelvin\per\mole} + 2\cdot \SI{33}{\joule\per\kelvin\per\mole}) - (2\cdot \SI{27}{\joule\per\kelvin\per\mole} + \SI{6}{\joule\per\kelvin\per\mole}) \\
\Delta S &= \SI{247}{\joule\per\kelvin\per\mole}
\end{align*}
%
Not so fine
\begin{align}
\Delta S &= \sum(S^{\ominus}(\text{produkter})) - \sum(S^{\ominus}(\text{reaktanter})) \\
\Delta S &= (\SI{214}{\joule\per\kelvin\per\mole} + 2\cdot \SI{33}{\joule\per\kelvin\per\mole}) - (2\cdot \SI{27}{\joule\per\kelvin\per\mole} + \SI{6}{\joule\per\kelvin\per\mole}) \\
\Delta S &= \SI{247}{\joule\per\kelvin\per\mole}
\end{align}
\end{document}
Which gives the following:

In the first set of equations, I've removed the numbering with the * sign, while in the second set I have not. However, I have the showonlyrefs=true option set in mathtools package, which usually removes all numbering of equations, unless it's being refered to. I would guess, that the long equations move the number to the next line, but somehow mathtools can't remove that space.
Is this a bug or am I missing something here? I rather like the way I can remove numbering when it's not needed, so I'd rather not go back to manually managing which equations I'd like to be numbered.

\textwidth, as you can check with theshowframeoption ofgeometry. If you set, say,hmargin=3cm`, it's OK. – Bernard Sep 25 '14 at 18:54mathtoolsshould, in my opinion, work as \begin{align*}, aka remove the line where the number "should" be. – Argo Sep 25 '14 at 18:59aligndecides that the second line is too wide, so it must typeset the number in a lower position; theshowonlyrefs=trueoption simply suppress showing the number, but it can't influence the decisions made byalignabout its position. You need to split that second line anyway, for example with\begin{multlined}[t]– egreg Sep 25 '14 at 21:49