This is due to the sub-equations being numbers using \alph, and there are only 26 choice a, ..., z. You can use the alphalph package to increase this enumeration using a a, ..., z, aa, ..., zz, aaa, ..., style sequence.
The default subequation numbering uses \alph, which can be patched using etoolbox:

\documentclass{article}
\usepackage{amsmath}
\usepackage{alphalph,etoolbox}
% \patchcmd{<cmd>}{<search>}{<replace>}{<success>}{<failure>}
\patchcmd{\subequations}{\alph{equation}}{\alphalph{\value{equation}}}{}{}
\begin{document}
\begin{subequations}
\begin{align}
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c \\
f(x) &= ax^2 + bx + c
\end{align}
\end{subequations}
\end{document}
\alph{cntr}and cntr>26 – Werner Mar 11 '16 at 00:48