It has been a while since I have played, but I don't think there have been any updates since I last played. I am working mainly from memory, as I am only in Phase 3 on my second playthrough.
Mushrooms:
I think there is a description somewhere (the mushrooms, or one of the processors) stating the mushrooms needed to be processed before they could be used. I assumed the description was wrong since mushrooms (and worms) can be put into the fridge.
Interior lights:
The walls don't block light. The interior is lit up by daylight when internal lights are off.
The external lights do illuminate parts of the interior at night if the internal lights are off. E.g., the external right on the other side of the wall from where the air scrubber/O2 tank/battery bank is at.
A quick test (luckily morning Phase 3 on my game) shows rover lights do shine through walls, illuminate the interior, and apparently can illuminate exterior portions of the base on the other side of the wall the rover is facing. (was not expecting that)
Rovers:
They don't seem well suited for 'long range' trips, but I never had issues with running low on fuel. But then again 'patrolling' sounds like a waste of fuel. I only used rovers for transportation, to do missions, prospecting, mining, etc.
Missions
I don't recall ever having trouble finding things. But then again, doesn't the PDA normally list location data for stuff like objects placed by secondary missions? Been a while since I played MC:C long enough for a mission to pop up, so I cannot recall if the PDA does show such info or not.
Missing items
No items vanished that I noticed (aside from the one relating to picking up a carried item when already having a carried item), but in one session I used a few items for crafting, when when I loaded the game the next session, one of those items was back in inventory. This was one or two versions ago, but I don't recall it happening again afterward.
Repair button:
I had the repair button on the rover glitch up 'once' during a repair, but repeatedly clicking on it did not boost skills, and game had to be terminated as I was stuck in the rover repair screen at the time. This was a few versions ago and might have been fixed as I never encountered it after that one instance.
Multiplayer issues.
Cannot help there, I have only played single player.
A pair of minor bugs I strayed across.
Early Phase 3, had to use the ELS to eat. Base was 'almost' pressurized at 13 PSI. When door to ELS closed, interior pressure 'dropped' to 9 something according to the suit info. The ELS control panel however showed 13.1, and the room quickly pressurized in under a second, so the suit reading of 9 was definitely wrong.
Second one, went to pick up a comm relay (I had first moved them into the entry room, next to the EVA locker), and it showed as held, but the one I was looking at was still there, I had assumed it instead grabbed the 'closer' one out of view to my character's right. When I went into the airlock to 'place' it, nothing happened, but the icon vanished, and nothing was placed. Checking back in the main room all three were still there, where I had first moved them to.
Edited: Found a second bug, tweaked one other thing.