Well, collies make an incredible amount of noise when they sleep. Mine sounds like he's dying half the time he's asleep, it sounds like the demons of He** are being unleashed.
There are a great many possibilities. Someone passing by in a car, mice in the walls, the dog had a seizure and felt weird when she woke up, there's a million things. The dog could be in a lot of pain from swallowing something or being ill.