What do I do about puppy pooping while in crate?

It could be the fact that you changed her diet to quickly and it upset her stomach causing her to have diarrhea that she can't hold. Any diet changes need to be done slowly by adding only a little bit at a time over the course of a week or more so the animal can adjust to the change. Since she isn't having accidents during the day you have at least part of the problem solved of house breaking. I would try taking this pup out just before you go to bed to see if it has to go if you aren't already doing this.