When you're using intersect to do what you have described you need to ensure you have inputs of either two polyshapes, a polyvec, or a polyshape and a linsegment as described here. Your input was two arrays and so you ended up doing a set intersection which has it's own seperate documention.
Try the following:
A = polyshape([2 6 4 2 -1 0], [0 -1 2 4 6 2]);
B = polyshape([0 6 6 0], [0 0 6 6]);
C = intersect(A,B);
figure(), plot(A)
hold on, plot(B)
plot(C,'FaceAlpha',0,'LineWidth',3,'EdgeColor','red')
