Instinct will lead to your dog digging in her bed and can be connected to the following:
Body Temperature
Should your dog be hot or cold, digging may be a way to create a warmer or cooler place to rest. The instinct to burrow into the resting place is natural and may be evident with a dog scratching at a hard floor or pawing at her bed.
The Desire to “Mark” the Bed
The foot pads of your dog have glands in them which emit an odor unique to your dog. When your dog digs or scratches the area where she is going to sleep, it allows her to mark the area with her scent.
To Hide
Your dog’s instinct may be telling her to dig a den that she can then hide in. If she were living in the wild, her effort to dig this spot would create a place that is comfortable for her to rest in while she can remain hidden from other animals. While this is not necessary for a dog living inside a home, the instinct is still present and can lead to this behavior.
To Create a Nest for her Puppies
Female dogs, whether or not they are pregnant, may dig to make a nest for their puppies.
Comfort
Just like we fluff our pillows and arrange our bedding to our liking, your dog may do the same thing. An arthritic dog in particular may circle and dig at the bed in an attempt to make the pain lessen.