In this case, you should specify which axes to plot on. See the example below:
%Initialize the figures
Gx = gobjects(1, 4);
Ax = gobjects(1, 4);
for k = 1:4
Gx(k) = figure(k);
Ax(k) = axes(Gx(k));
end
%Plot to the Nth figure
for k = 1:4
plot(Ax(k), rand(1, 10), rand(1, 10));
^ INCLUDE AXES HERE! %To plot to 1st figure, use Ax(1). 2nd figure, use Ax(2). etc.
end
