You can reproduce the issue by running the following. If you set a break point on the last line, you will see the subplot disappear after executing the last line.
d = dipole;
[efield,az,el] = pattern(d, 75e6,'Type','efield');
phi = az';
theta = (90-el);
MagE = efield';
This behavior occurs because the default to visualize radiation pattern is set to polar. If you look at the source code of 'patternCustom' when using 'polar' or 'rectangular', the current figure will be deleted.