[Yorkie4luv]

Hmm, well you now have a new "baby" she maybe a baby in furry form, but she is still a baby and as you know babies wake up and cry at night.
I put mine in the same room with me and when they cried I would just get up and hold or pet them and reassure them I was there and tell them in a soothing voice "shhhhhh go night night" to this day they know that "night night" means to go to bed. She maybe just waking up and feeling scared when she realizes she is all alone. Do you take her outside before bed and make her go "potty" outside? that may help too, as she may not like the smell of the "potty" in the pen. Hope some of this helps!
Once I knew they could hold their potty through the night I would put them in my bed up by my head, to be sure not to crush them...but that's only if you eventually want her sleeping with you.