Railgun Compartment cannot be fixed by bots.
Rear gunnery is missing one gap.
Bots are getting stuck in a command room.
Bots have touble getting to the goxygen generator, because of misplaced waypoint.
Railgun supercapacitor is inaccesible.
Bots often lock the doors and can't unlock it.
Junction room has wonky gap placement leading to water not flowing properly.
Shell cap A vertical in the command room can be destroyed and won't cause leaks.

It's a giant ship so i'm not done testing leaks and waypoints.
Also the hulls are off the (snapping) grid in many places.

@LazyName

-Railgun Compartment supercapacitor is fixed, assuming this means it can be fixed by bots.

-Rear Gunnery Gap is fixed

-Bots stuck in command room. They didn't work well with the platform and the slanted shell so I removed the waypoints from them to go down there. However they can still repair the pump from my test by standing ontop of the platform.

-fixed O2 waypoints for NPCS --> They climb the ladder properly now.

-Door locks -- I am testing a fix to see if raising the buttons will make it out of the NPCs reach. I didn't have issues with it prior but maybe it being out of the hitbox for the actual door buttons will work.

-Junction gap is fixed

-Shell cap A vertical in the command room does cause leaks when destroyed for me -- I don't know how to approach this one.

Some Hulls have been slightly readjusted but most are placed off grid because I get picky down to the line. But they should be fine, atleast in my testing they fill and dispense properly after these fixes. Posting the update soon. Thank you for highlighting these issues for me.

When shooting shell cap A from inside the hull will damage the overlapping floor and not the shell. Shell can be easily damaged from outside and allows to shoot inside the sub with no leaks.
I fixed the overlap and it works properly.

When I complained about hulls it was a nitpick. I often edit the subs I use and having many things off grid makes it hard to do so.

Bots in the command room was fixed by forcing the bots treat incline like stairs. Disconnecting the upper waypoints from the lower fixed the issue.

Supercapacitor should be fine as long as anyone can interact with it.
I think there's misunderstanding, hull linked to the railgun compartment cannot be accesed by bots and thus unfixable.
I slapped a ladder and a small platform on there and it's all good.

I'll update and see where to go from there.

Captains Room 3rd hull doesn't have a waypoint so AI won't fix any leaks in that area. => Move waypoint 3531 to the adjacent hull.

Security Room's last hull has the same problem, with same solution of moving waypoint 3331 to the problematic hull.

Engine one has the same issue, but in this case additional waypoint is needed.
Oxygen Generator Room has the same problem.

The fix in pathfinding in the command room caused so AI won't reapair the bottom. The hulls there need waypoints. Adding waypoints there and connecting them to waypoint 3192 should solve it. But in my testing I couldn't find any satisfactory solution.

UPDATE: I found a solution! It's not waypoints but hulls that need change. Trim the main command hull to the right, and extend both lower hulls up. Put some gaps in and it WILL work.
UPDATE 2: The bots still need waypoints to get out of the hole in command room. Bots are trying to navigate to the waypoint in a adjacent room and ignoring the wall. I found a setup that works well enough, bots get stuck only for a sec before taking a different route, so that's a possible fix.

In general if there is no waypoint in a hull, the AI won't be able to pathfind to any damage the hull is taking.

I was experimentin with the railgun compartment issue and I figured out that changing the hull layout will fix the issue. Extend the problematic hull downward and trim the ralgun compartment to the side, this should fix it.

Pumps emergency drain function doesn't work when sub is on manual steering, Is this intentional ?

There is a one giant hull in the mid acces shaft instead of 2 smaller ones. I see no potential problems with that other than visually water appearing to come from not flooded parts. (ex.: water floods from the top of junction room when only bottom door is open)

If you need screenshots let me know.

Here are more nitpicks. :p

Reactor controler's greater than component has 20000 output, causing meltdowns at anything more than one uranium fuel rod. Changing this to 12500 casued meltdowns at 100% engines with 4 thorium fuel rods.
Changing this to 10000 makes the reactor handle smoothly.

Talking about smooth, lower duct in the ballast hallway is leaking water from the ballast, causing the ballast pump to never reach 100% flooding and causing erratic power draw. (Not something major)
I don't know how this could be prevented, but this is caused when the ballast is roughly 40% flooded and the duct is triggered. Simply pumping out the water fixes the issue.
Total nitpick, tried to eliminate the erraatic reactor load, but i think that's just how it works

I don't think there is a engcab tag on any of the lockers as bots throw welding tools and fuel rods into the armory cabinet.

Thank you for all the fixes I need to do. I haven't had much time recently to get to it and probably won't for the next couple days. I will try and fix it when I have free time to do so.