Our puppy is 9 weeks old... we have had her for a week. Unfortunately, she has been pooping in her crate the last 3 nights. I am not sure if this is separation anxiety as she sleeps in the crate with our other dog (they are both small and sleeping together has caused her not to whine at night). She gets fed in the morning and we always let her out at night before bed (around 10). I know NOTHING about puppies, we got our other dog from the pound and she was about 10 months old. Will this stop with time or am I doing something wrong?

Make sure she walks around on her last trip outside for the night. Walking stimulates the body. It is common for a new puppy to have a few accidents in its crate, but it is possible she may have developed bad habits from poor care before you got her.

You should be feeding her 3 times a day until she is 3 months old.

There is some good material for a new puppy owner in the sticky at https://www.askmehelpdesk.com/dogs/information-articles-our-dogs-expert-labman-53153.html

Thank you for the info regarding new puppies. Actually, we separated the puppy from our 3 year old dog and found out that it was our 3 year old dog that was doing the pooping! I could not believe it. She has never done this before. She happily plays with the puppy all day... could she be jealous? We really don't pay more attention to the puppy! We always pet the older dog too and tell her she's a good girl. What do you think?

It usually takes a dog a while to accept a new dog in the family. You are correct in continuing to give the old dog plenty of attention. It is possible you haven't given it the leadership it needs. A top dog have the right to bring in new pack members. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at Raising Your Dog with the Monks of New Skete (http://www.dogsbestfriend.com/) For more on being top dog, see Establishing and Keeping Alpha Position (http://www.dogbreedinfo.com./topdogrules.htm)