I created a minimal test game rule mod for this issue.
You will see that the shipyards will attack the resource collectors, but that they will do zero damage.
It could be that the test mod is too minimal, and that I am missing an important file. I’m not sure. It also happens versus probes and other non-combat ships. Could it be a family issue?
The problem is not just with not taking damage, but with projectiles always missing. I ruled out it being a .ship file issue by saving the “hgn_mothership.ship” file over the “hgn_shipyard.ship” file (and making a few necessary adjustments). Could the hull defense gun hardpoints be misaligned? Compare the accuracy of the Hgn_Mothership which has the same guns but kills interceptors 20x faster.