I think the problem comes from a blank line in your matrix (after your last line of entries in your matrix). The following works fine for me:
\definemathmatrix
[pmatrix]
[left={\left(\,},right={\,\right)}]
\starttext
\startformula
A = \startpmatrix
\NC 11 \NC 12 \NR
\NC 21 \NC 22 \NR
\stoppmatrix
\stopformula
\startformula
M^3 = \startpmatrix
\NC 2 \NC 3 \NC 6 \NC 4 \NC 2 \NC 7 \NC 3 \NC 1 \NR
\NC 3 \NC 0 \NC 1 \NC 1 \NC 2 \NC 3 \NC 6 \NC 4 \NR
\NC 6 \NC 1 \NC 4 \NC 4 \NC 4 \NC 9 \NC 10 \NC 6 \NR
\NC 4 \NC 1 \NC 4 \NC 4 \NC 5 \NC 8 \NC 8 \NC 3 \NR
\NC 2 \NC 2 \NC 4 \NC 5 \NC 2 \NC 7 \NC 3 \NC 1 \NR
\NC 7 \NC 3 \NC 9 \NC 8 \NC 7 \NC 8 \NC 10 \NC 3 \NR
\NC 3 \NC 6 \NC 10 \NC 8 \NC 3 \NC 10 \NC 4 \NC 1 \NR
\NC 1 \NC 4 \NC 6 \NC 3 \NC 1 \NC 3 \NC 1 \NC 0 \NR
\stoppmatrix
\stopformula
\stoptext