She might be waking up and feeling a bit lonley. Maybe you can give her a cuddly toy or a safe chew toy to keep her busy during her "awake times".
As Fasteddie noted, you could always move her to your bed but then it's a lifetime change for both you and your Yorkie pup. She will forever want to be in that bed. Also, if you choose this route, make sure she doesn't jump off the bed, bad for their legs/knees.
If she is real young she might be needing to relieve herself also.
Sorry to hear about the lack of sleep, it will get better as your pup matures.
