I ran into another problem on mission 6-4. I'm only supposed to scan Nav, Weapons, and Sensors. Yet every subsystem is now scannable (even every engine). Even every turret is originally marked "not scanned".
When I scanned Weapons, that objective was not made blue on the directives list (i.e., it wasn't marked as completed). Something else that is weird, when I scan one component of the Royal Sathanas, every subsystem (when I then cycle through) is marked as scanned, so I don't have the opportunity to scan the other two required subsystems. There seems to be something wrong with scanning on this mission.