For example, Focused Distruptors gained with Distruptor tech, can never be added to Starbase without it having Hyper-Phasors. But none of the races with Distruptor tech have Phasors.
There are several other "holes" too.
Races that have Sigularity Driver techs can't add Neutrino Snipers (gained with Black Hole tech), since they require Gravitron Snipers added first (which require Graviton Driver IV tech these races have no access to).
Also, races that don't have Lasers or Rail Guns, can't get Laser Equalizers or Sniper Turrets, so they could never build Hyper-Phasors or Gravitron Snipers if they are in their tech tree.
And Thalans can't add Sub-Space Warheads, since they require Missile Launchpads, which are gained with Missile Weapon Theory they can't research.
Probably the easiest way to fix this would be delinking all attack-assist modules that are gained from weapon tech tree from each other.