For work I am doing, most of the "automated tools" are things I wrote myself and I know what they do. It is up to the engineers working on the engagement to exercise care and avoid causing disruptions to the target or doing things they can't reverse easily.

I like to remind people that having someone on retainer that breaks your stuff with an automated tool is better than having some random guy on the internet break your site with the same tool. Either way it is eventually going to happen, but at least I will immediately notice and contact the right folks to help get it fixed.