By the way, is there a readme or something? I can't find any instructions for the new systems, and I still haven't figured out how to make NPC strike craft dock.
Instructions for what? WINGCOM is documented in game in the intel screen and on the main page. Strikecraft stuff is pretty self-explanatory (but I am the developer, so let me know if there is something that isnt

) Like SpaceDrake said, they dock when they need to
Btw,when your mechs are loaded with missiles And the missile runs out of ammunition,they will return to the mother ship to resupply when they are in good condition or other weapons have plenty of ammo.
While this isn't optimal, its the same behavior that vanilla fighters have (well, I guess not 100%, since fighters continue to attack on "engage" until you flip it, so maybe I can add another condition such as having no target)
Also, regarding the bug:
I wasn't able to reproduce it.I tried with both the ship AI controlled with and without an officer, as well as being directly controlled.
Maybe there is something I am missing?