We had this same problem with Dori when she was about that age. What we did is made sure she didn't have any solid food within 2 hours of bedtime, took her to the pottypad and outside to have a bowel movement before bedtime, (if she would) and she eventually stopped. She had two crates, one smaller and the medium size. T he medium size was the one she would poop in. So, we put her back in the smaller for the nights. I think these changes helped, she stopped in about 3 nights after. It is definately annoying and smelly
Is your baby laying in it or going in a spot in the corner of the crate?