Playing the Official Balance Mod vs. the CPU. It seems that the Vaygr have issues damaging the HP of the core module of both Taiidan and Kushan Research ships. Their missile and cannon shots impact on the expanded research modules and do not do any damage to the core ship’s HP.
This results in the Vaygr Destroyer, Heavy Missile frigate, Laser Corvette, Bomber, and other projectile ships not dealing appropriate damage. They have to chew through the surrounding expansion modules that are blocking the shots before they do actual damage to the structure. I’m not sure if this is affecting other factions as well.
The one exception is the Vaygr Battlecruiser’s Trinity cannon which seems to aim specifically at the core module and does the expected damage. However, Its 8-tube heavy missile battery suffers from the same problem as other ships and does not do any damage to the core HP.