I used to have the same issue with my game, though mainly with items placed on the wall. The game saw them on the wall, but I didn't. After a couple of panic moments where a legacy painting got 'lost' I stopped hanging anything sim made (paintings, sketches, photos, etc). Have you tried saving your game (save as, don't override your main game), quitting Sims 3, and re-loading? That made my paintings re-appear. Of course, I then pulled them off the walls and never hung anything again, so it's not much of a solution!
Do make sure you're patched up. This issue happened to me months ago, back when I also had the photography bug (sims getting stuck taking pictures) and just about every World Adventures bug possible. With the latest patches the majority of the old bugs are gone, and I'm experiencing the joys of picture taking, tomb raiding, and photo hanging for the first time.
I know multi-generational family saves can get huge and cause glitches all by themselves, so that's also a possibility (but I don't know of any solution to it).
If you can't move the rock or old paintings and want to build, you can try using moveobjects on, or some of the other testingcheats commands to try and delete or move the invisible objects. If you can get to the point where they're visible, even if they can't be interacted with by sims, you might be able to ctrl+shift+left-click the object and choose 'delete' from the radial menu. The object will be destroyed but building should be possible once it's gone.
Hopefully patching takes care of it, and if that doesn't work I'd strongly suggest you keep all legacy items in your sims inventory until it's over! Good luck!