All the carrier definitions in the ShipBlueprintDefs.xml file specify armor, but not the other defenses. So either the armor defense should be removed or the others should be added.
I think it is a remnant of the change that Paul temporarily made to have armor defend against all damage.
Fix: add the other defense to the carrier blue prints.
<ComponentType>PointDefense</ComponentType>
<ComponentType>Shields</ComponentType>