What did I miss there?
Building a ship with enough on-board maintenance supplies to fix it.
In other words, both of your cases are working as intended. Think about a wet-navy ship that uses a single jet-turbine engine as its power source. If the turbine breaks and you don't have a spare on board, you're in trouble. There are two broad categories of reason the turbine might break:
1) Poor preventive maintenance, e.g. you didn't replace an oil pipe when you should have, the pipe broke and spewed oil into the engine, which caused an engine fire.
2) Combat damage, e.g. it got hit by a bomb.
The idea behind maintenance costs is that it's cheaper to prevent a failure than to fix one that's already happened. So the 1xfailure cost represents the overhead of keeping all those spare pipes around. The 2x cost represents the cost of keeping the whole turbine around (i.e. fixing it after it broke). A fundamental principle of Aurora is that ships require on-board support systems; they aren't just guns on engines. In your "cheap grav ship", you chose to trade capability/cost off against the risk that if the ship breaks you won't be able to fix it. The scenario you describe (right up until you SM'd in a new ship) is exactly the sort of situation that occurs in real navies - you didn't have the on-board resources to fix it, so you had to choose between getting it home some other way and scuttling it.
In the second case, repairs need to be done at a SY - the overhaul is a lower level of refit that is done at maintenance facilities (think of the engine replacement case again - you don't get an engine job for your car at jiffy lube). You can put a suggestion in that Steve somehow provide a warning that X didn't get fixed in the overhaul, but other than that I think it's unlikely the mechanics will change. Aurora went through a LOT of gyrations trying to balance micromanagement burden and "reality" in the early days, you can probably find some of the threads if you search 4-5 years back. And now that you've discovered that overhauls don't do repairs, you won't run into that issue again
As a general rule, it's a good idea to keep supplies for the most expensive component on board for non-combatants (who aren't expected to need to fix combat damage) and 2x the most expensive for combatants.
John