It seems that \NC in mathalignment is looking ahead for the next \NR, because 
when I wrap the matrix
in an explicit brace group it works fine again:

\definemathmatrix
  [pmatrix]
  [left=\left(,right=\right)]

\starttext

\placeformula
\startformula
  \startmathalignment
    \NC \sigma_x \NC=
    {\startpmatrix
      \NC 0 \NC 1 \NR
      \NC 1 \NC 0 \NR
    \stoppmatrix}
    \NR[+]
  \stopmathalignment
\stopformula

\stoptext

On Tue, 2017-06-06 at 10:26 +1200, Henri Menke wrote:
> Dear list,
> 
> When I have a mathmatrix inside a mathalignment the numbering using \NR[+] 
> does not work anymore.
>  Instead it prints "[+]" on the next line.  I guess the definition of \NR 
> from mathmatrix leaks
> outside.  Affects both TL2017 and latest beta.  MWE is below.
> 
> Cheers, Henri
> 
> ---
> 
> \definemathmatrix
>   [pmatrix]
>   [left=\left(,right=\right)]
> 
> \starttext
> 
> \startformula
>   \startmathalignment
>     \NC \sigma_x \NC=
>     \startpmatrix
>       \NC 0 \NC 1 \NR
>       \NC 1 \NC 0 \NR
>     \stoppmatrix
>     \NR[+]
>     \NC \sigma_y \NC=
>     \startpmatrix
>       \NC 0 \NC -i \NR
>       \NC i \NC 0 \NR
>     \stoppmatrix
>     \NR[+]
>     \NC \sigma_z \NC=
>     \startpmatrix
>       \NC 1 \NC 0 \NR
>       \NC 0 \NC -1 \NR
>     \stoppmatrix
>     \NR[+]
>   \stopmathalignment
> \stopformula
> 
> \stoptext
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