Im sure it happens because during the ruins generation, the game selects a random stone material to build the walls/floor from. Completely random. And since lunar maria/highland rocks do qualify as stones in the code, the game selects them to build the ruins from.

I don't know if this can be fixed or not, I'm guessing it's hardcoded. Then again, I'm not a developer, I simply know this fact, thought you might find this info useful.

It isn't just ruins, but stone in general. Still, would be nice to add some code to exclude lunar type rocks from map stone choice. Sadly, likely some hardcoded issue. I guess alternatively could remove "lunar types" from normal stone material code and then only apply it upon lunar map generation (since building dish or whatever is necessary for lunar map generation), but that might be too much work for just some mod (if even possible).