Kids aren't going to be on their best behavior 24/7, almost especially when you really want them to be. The beauty of a documentary session is that they don't have to be. They are allowed to just be whoever they are, and it takes a ton of pressure off you. I'm not saying don't parent them, but you shouldn't feel stressed about keeping them still, clean, happy, and so on all the time.
And honestly, I kind of love it when kids do "misbehave" or get upset during a session. Okay, I feel like I need to explain that more. I don't love that they are going through a hard time, or that you are. But I do love showing what the everyday life of your child is like, and I love seeing them as who they truly are. And I love seeing the connection between a parent and child when they are going through those moments.
I have to admit that I don't find it easy to photography my own children at times because of this. If I really put on my photographer hat around them, I find I have to let some things go that I normally wouldn't! In this picture you can see my son about ready to honk the horn in a parking lot. The second after I took this the next word out of my mouth was "Don't."