Over-organizing?

I tend to organize my layers so that other people (or myself) can easily find their way in my files. I'm working on this complex page for a social media web site and when I was dragging a group of layers from one file to another I got this alert. Never had this before. I checked the layer group nesting and I go 5 levels deep, but like I said, it's a complex site with a ton of different user interaction scenarios. Am I going overboard here? I say you can never be too organized.