We’ve seen it many, many times: the ship gets into a firefight, takes a few hits, shakes around, and consoles explode (possibly taking an unfortunate ensign with them). Eventually the battle is resolved with our heroes largely intact if somewhat shaken up. If it was a particularly nasty battle, there will be signs of damage: scorches on the walls, deformed equipment, busted lights, and rocks scattered about.
All of that seems reasonable… except the rocks, which look pretty out of place in a spiffy 24th century starship. So why are they there?
In the 32nd century, my headcanon is that the programmable matter is just bricking into something that looks like rock.
For the 24th century, conductive concrete as a Faraday cage and frame for the bridge modules. (…and yes conductive concrete Faraday cages exist in real life, even if they’re not quite the same shade of gray).