Oh no, I let this thread slip to page 2 without reporting any more bugs!
Well here's a bug, and an idea:
Small rocket pods are useless (one shot, 7 damage, ships/planets only?), while all other fighter/shuttle weapons besides shuttle phasers are rather dubious - or have I just not researched enough? At least the torpedoes should be useful; shuttles are commonly armed with mini-torpedoes...
How about anti-seeker weapons for fighters/shuttles, and maybe vice versa? Neither seekers nor fighters are common in Star Trek, but since they're in, it seems to make sense that one could hit the other...