Make resources required for items and stuff too. What kind of gun would use stone in its construction? You'd need some metal (for the mechanisms/barrel) and some wood (for the body) to make a rifle.
Stone wouldn't really be used in item manufacture so it'd be a good thing to use for building, but since it's harder to get than wood you'd need to use some wood too or spend too long finding materials.
Wood would also be used for fire, and be flammable as bricks go, whereas stone isn't flammable, making it a more useful candidate for building in that respect also.
Bullets would be able to chip away stone, so you could destroy a stone base with some work, but metal would be basically indestructable for that purpose, and thus adds the extra security, however it's used in item manufacture and is somewhat rare. Wood, of course, would be easy to destroy, especially using melee weapons (ax/sword) so a wooden base wouldn't be very secure at all, however it'd still be better than nothing.