Sometimes baby chicks will eat shavngs. I always use paper towels until they are a little bigger. I used to put the paper towels on top of pine shavings but it makes the food and water spill too easy.
Mine started to have this problem a couple days after I got them. I added some corn meal to their food with a sprinkle of grit and put them on pine shavings. That worked for me.
For the first 2 wks of life my chicks start off in a wire brooder. I put some pine shavings down with some DE in it and it helps dry up the poop and not so smelly. I haven't had any poopy butt. Also having the chicks in the litter, helps the chicks in resistance to cocci. I have never had any problems with any of my chicks.