[Ulzgoroth]

I think the biggest and fatal fault is the way it uses standard GURPS rapid fire rules for attacks from batteries of weapons and for attacks spread over multiple seconds. This is particularly bad whenever missiles and point defense are involved. This has a few knock-on sub-murphies, but those would likely vanish in the process of getting rid of the core problem.

Spaceships combat has two-axis scalability (time and space). Unfortunately, it doesn't necessarily conserve important features of combat over scale changes. Ignoring the time-scaling issues with weapons previously noted, there's a problem with Dodge. To be allowed to dodge under either combat system, your ship has to use a certain amount of thrust. How much is dependent not on any property of your ship or the attack to be dodged, but rather on the combat scale in use. I'd suggest simply setting a constant minimum delta-V that must be burned in a turn to allow a dodge, and allowing that to be burned whether or not it's sufficient for the ship to accelerate significantly at the combat scale.

The economics of building spaceships, or of anything built by spaceships factory systems, are pretty much absurd. Occasionally outright physics-breaking, as in the refinery which can electrolyze water fast enough that it generates more fuel than a fuel cell powering it consumes.

There are some smaller peculiarities:
-What's the rate of fire of Spaceships weapons in regular GURPS combat?
-Should any imperfect landing be catastrophic? A crash landing does 6dx3xHPx0.1, which averages 6.3xHP. Any other landing is non-damaging.
-The description of Steerage Cargo calls into question what regular cargo space is. And by talking about carrying livestock, also the rules for life support capacity.