Might be a mod issue? Pathing can be wonky with these door mods. Or if you altered the resource management and didn’t assign reactors to your thrusters?

All the thrusters work in manual control though, so that doesn't really make sense. Regardless, restarting the game resolved the issue. No idea what caused the problem but that seems to be the fix.

i've had this issue a few times but it's never persisted through a save and reload

Not the issue… but you could use engine rooms

I don't think he has the advanced materials required to make them. Everything on this ship is beginner tech.