AMS Split inside AMS Align

I don't know what you are trying to achieve. Your error message can be bypassed if you either increase the number of reference points in the alignat

\begin{alignat*}{2}
= & \begin{split} x+ \\
y\end{split}
\end{alignat*}

or if you use aligned instead of split

\begin{alignat*}{1}
= & \begin{aligned} x+ \\
y\end{aligned}
\end{alignat*}

With split, it tries to anchor its & to line up with the ones outside (so multiple splits inside one equation will line up). So implicitly you need one extra reference point if you use split inside alignat, which is just a glorified array. (I'm doing a horrible job explaining this, am I not?) aligned doesn't try to do that (two aligned blocks inside one equation won't line up), and so you can get by with just one reference point.

In anycase, either of this sets the broken expression x+y as one unit to the right, vertically centered, against the = sign, which I suspect may not be what you want. If you want the = to line up with the x+ and with the y in a line below, you should take Lev's suggestion.

It's not clear what effect you're trying to achieve, but it is certainly possible to use split inside align, for example:

\begin{align}
  x &= a+b\\
  \begin{split}
  y &= a - b\\
    &\quad +c-d\\
    &\quad +e+f
  \end{split}\\
  z &= e-a
\end{align}