Oh my god finally someone mentions this! I thought I was going crazy. What I've seen in my current run is not exactly what is described but does sound freakishly similar.

I have this base, kind of built up yeah but not crazy either (~3000 instances or something) and once in a while, totally randomly, I have this torch and sign that just breaks. I would go on an adventure and come back, or just log into the game and I would find the materials (copper, wood and coal) just there on the floor. The torch and the sign, placed next to each other, just decided to self destruct while I was away.

It's always these 2 objects. This has *nothing* to do with structure integrity (other than a bug of course) since this happens on my 2nd floor and my house has 3 floors.