Items/NPC's getting stuck in rocks.

It seems as the longer a server runs without being wiped, the more resources(?) and npcs get stuck after spawning inside of a rock where nobody can interact with them.
I didn’t see anything on the trello about this, and was wondering if there was a way to reset a server without wiping it. Does restarting it have this effect?

Bonus picture of what you should do when you find anything stuck anywhere:

http://cloud-4.steampowered.com/ugc/3372369252279346659/6F6C095ABB69DF9603CCB38C49057E8D38023B92/

This bug is normal and appears on every server.
You can’t do anything against that.