How large is her kennel? Sometimes puppies will poop in their kennel of its too large. You want it big enough so that they can stand up and turn around, and not much bigger. That's why a lot of large dog crates come with a divider so that you can enlarge their area as they grow. She may also need to be taken out more frequently. Pooping in her kennel could also be a learned behavior if she wasn't given adequate breaks to potty where she was previously kept. Puppies should be taken out at least every couple hours and within 15 mins or so after each meal to give them a chance to potty.