Thanks for starting this thread! I've been thinking about prepping a similar session after watching the first season of The Expanse, so I'm excited to read what others think about this.
To me, what makes a submarine / spaceship situation so interesting and tense is the fact that you're trapped in a small metal box that is entirely surrounded by something that will kill you in a matter of seconds/minutes: water, space void, radiations or whatever you can come up with that adds a bit of spice to this situation
If a single thing goes wrong on the ship, everything can and probably will go south very quickly. I see two sides to this:
1- Mechanical failures
The engine fails and you're basically stuck where you are or on your existing trajectory. So what if you're already short on resources and risk running out of energy for the life support systems, or food? Or an obstacle is coming your way and you have to find a way to avoid a collision?
If you have a comms failure, you have no way to get help.
If the hull's integrity gets compromised, parts of the ship become unavailable or much more dangerous to access. And once it starts, it usually doesn't get better.
2- Human failures
just thinking about their situation and how many things can go wrong would make any inexperienced sailor completely freak out.
If some some PCs or NPCs are taking their maiden trip, or have anxieties / environmental or social phobias related to the situation (claustrophobia, agoraphobia, etc), you have some great hooks for more interpersonal drama. It would also give interesting opportunities for the party's Face, unless the Brute knocks everybody unconscious first!
You can even combine the two by having an antagonist inside the ship messing with things and making everybody suspicious / on edge.