Have you by chance had an enemy (such as a rhino-clockwork, or a giant like bearger) run over a pile of stones by chance? With "natural" stone spawns -> boulders/mines turned on, it causes a rather crazy explosion of created boulders and mines when an NPC runs them over, which in turn creates more of them, which then get run over, and the NPC and the boulders/mines leap up into the air until they finally stop moving.

It's really bizarre and kinda funny, but I had to disable turning spawned rocks into boulders/mines. Q.Q