The easiest way, assuming R2017b or later, is to use the intersect method of the polyshape object, which you can construct either by providing the 4 corners of your perimeter or with nsidedpoly:
perimeterside = 0.2;
for blackdotidx = 1:size(B, 1) %iterate over the black dots
perimeter = nsidedpoly(4, 'Center', A(blackdotidx, :), 'SideLength', perimeterside);
if ~isempty(intersect(perimeter, A))
%1st output of intersect is segments inside the perimeter, so if not empty there is intersection
fprintf('trajectory intersect perimeter %d\n', blackdotidx);
end
end
