I know this is how people in the 80s and 90 imagined the future and a lot of concepts were probably too far fetched for them.
BUT... why arent they using drones to explore planets? why are there not more drone-spaceships? why does enterprise need a crew to begin with? Why is there so little automation? Why so few uses of AI in general?
I am saying this as a star trek the next generation person. I'd also expect them to have full video and sensory streams of any surface mission teams.
Option B
Rogue AI hidden in code.