With the following code :
\documentclass{article}
\usepackage{mathtools}
\mathtoolsset{showonlyrefs}
\begin{document}
\begin{align}
A & = B \label{eq:first}\\
& = C \tag{a}
\end{align}
Reference to \eqref{eq:first}.
\end{document}
I obtain the following result:
With \tag* instead of \tag, I have the expected result.
Of course, it doesn't seem logical to put \tag{a} without the option showmanualtags but the result seems strange.

showonlyrefs. Reasons are in order of importance. – egreg Jul 20 '18 at 11:40