Most significant problems ociated with discussions of divine activity in nature?

I was given this topic to write about my paper and was hoping if people could help me get started with it. We read a couple of different pieces such as William Paley's Natural Theology with the watch. This isn't a piece about how the idea of divine activity is problematic so please don't turn this into some huge debate about god and such. We have discussed things such as intelligent design and what not and I just need arguments against divine activity in nature. Here's an example if I have confused anyone: One argument against god in nature might be all the violent acts that occur (read about some of these in Darwin's Origin of Species). Other people argue that if god was in nature then why would he let bad things happen to good people. Once again I don't want people to read this and think it's an anti-god piece that I'm writing it was just an ignment given to me so don't turn it into something it's not. Thank you in advance for any ideas