In real life, if you have a rock that is partly buried in the earth, the exposed rock surface will be clean and dry. However, if you turn over the rock, underneath it you generally find moist earth that is usually full of worms and insects. If you study nature, you might want to do this! However, worms and insects are generally thought of as unpleasant--even dangerous in the case of spiders and scorpions. Collectively, using somewhat childish talk, we may call them "creepy-crawlies." Several idioms play on this idea:
"Don't turn over that rock."
"Let's not look under that rock."
"He looks like something that crawled out from under a rock."
Another expression along the same lines is "let's not open that can of worms." The idea is that once you've opened a can of worms, you can't put the worms back. In a discussion, it means "let's leave that unpleasant topic alone, because if we start to discuss it we'll waste the whole meeting talking about it."