CW stated that Bella kept getting out of bed that night to find out when Shanann would be home. I think that little girl was feeling a lot of insecurity and anxiety that night.
I can't imagine that weekend with their dad resembled anything that was normal for those little girls. He probably didn't even talk to them. He was probably very cold to them and I think he pretty much just threw cold pizza at them, and they probably had to remind him to feed them. He was extremely preoccupied with NK and he looked downright scary in the picture taken of him at the birthday party.
Bella was old enough to pick up on things, JMO. She may not have been able to go to sleep, heard her mom come home and got out of bed again.
JMO.