It's only drawing that connection because you didn't "lift the pen" between drawing the two platforms. You haven't told plot3 anything about the connections. You need to spell it out explicitly like this:
plot3([xplot, nan, ...
x1plot, nan, ...
xplot(1), x1plot(1), nan, ...
xplot(2), x1plot(2), nan, ...
xplot(3), x1plot(3), nan, ...
xplot(4), x1plot(4)], ...
[yplot, nan, ...
y1plot, nan, ...
yplot(1), y1plot(1), nan, ...
yplot(2), y1plot(2), nan, ...
yplot(3), y1plot(3), nan, ...
yplot(4), y1plot(4)], ...
[zplot, nan, ...
z1plot, nan, ...
zplot(1), z1plot(1), nan, ...
zplot(2), z1plot(2), nan, ...
zplot(3), z1plot(3), nan, ...
zplot(4), z1plot(4)], ...
'LineWidth',2)
Although I might go with something like this instead:
clf
h = patch(nan,nan,nan,'FaceColor','none','LineWidth',2);
view(3)
for i=1:50
t(i)=0.1*i;
P=[0 0 20]';
s=[ 0 0 1];
R1 = [cos(i*0.0174532) 0 sin(i*0.0174532)];
R2 = [0 1 0];
R3 = [-sin(i*0.0174532) 0 cos(i*0.0174532)];
R = [R1; R2; R3];
B1 = [ 15 15 0 ]'; %sph
B2= [-15 15 0]'; %rev
B3 = [-15 -15 0]'; %rev
B4 = [15 -15 0]'; %sph
A1 = [5,14,0]'; %sph
A2 = [-30,30,0]'; %rev
A3 = [-30,-30,0]'; %rev
A4 = [5,-14,0]'; %sph
b1 = P +(R*B1); %sph
b2 = P +(R*B2); %rev
b3 = P +(R*B3); %rev
b4 = P +(R*B4); %sph
%position%
x1(i)= dot((b1 - A1),(b1 - A1));
d1(i)= sqrt(x1(i)); %sph
x2(i)= dot((b2 - A2),(b2 - A2));
d2(i)= sqrt(x2(i)); %rev
x3(i)= dot((b3 - A3),(b3 - A3));
d3(i)= sqrt(x3(i)); %rev
x4(i)= dot((b4 - A4),(b4 - A4));
d4(i)= sqrt(x4(i)); %sph
%angles%
s1 = (b1-A1)/d1(i);
s2 = (b2-A2)/d2(i);
s3 = (b3-A3)/d3(i);
s4 = (b4-A4)/d4(i);
th1(i)=acos(s1(3)); %sph
th2(i)=acos(s2(3)); %rev
th3(i)=acos(s3(3)); %rev
th4(i)=acos(s4(3)); %sph
ss1(i) =dot((b3-A3)/d3(i),[0 1 0]);
ss2(i) =dot((b4-A4)/d4(i),[0 1 0]);
phy1(i) = asin(s1(2)/sin(th1(i)));
phy4(i) = asin(s4(2)/sin(th4(i)));
%animation%
xplot = [5,-30,-30,5,5];
yplot = [14,30,-30,-14,14];
zplot= [ 0 0 0 0 0 ];
x1plot= [d1(i)*sin(th1(i))*cos(phy1(i)) , ...
d2(i)*sin(th2(i))*cos(0) , ...
d3(i)*sin(th3(i))*cos(0) , ...
d4(i)*sin(th4(i))*cos(phy4(i)) , ...
d1(i)*sin(th1(i))*cos(phy1(i))];
y1plot= [b1(2)+d1(i)*sin(th1(i))*sin(phy1(i)) , ...
b2(2)+d2(i)*sin(th1(i))*sin(0) , ...
b3(2)+d3(i)*sin(th1(i))*sin(0) , ...
b4(2)+d4(i)*sin(th4(i))*sin(phy4(i)) , ...
b1(2)+d1(i)*sin(th1(i))*sin(phy1(i))];
z1plot = [d1(i)*cos(th1(i)) , d2(i)*cos(th2(i)) , ...
d3(i)*cos(th3(i)) , d4(i)*cos(th4(i)) , ...
d1(i)*cos(th1(i))];
verts = [xplot, x1plot; yplot, y1plot; zplot, z1plot];
faces = [1 2; 2 3; 3 4; 4 1; ... % first platform
5 6; 6 7; 7 8; 8 1; ... % second platform
1 5; 2 6; 3 7; 4 8]; % connections
h.Vertices = verts'; % note transpose!
h.Faces = faces;
pause(0.003)
%%%%%%%%%%%%
end