Here are some wild guesses at what might be wrong (bear in mind that I am not a vet):
Perhaps there is some minor pain that does not bother the dog during the day, but becomes more annoying at night, especially after not moving for a while. I have some minor aches and pains that come and go, that don't bother me too much during the day, but can prevent me from getting to sleep or wake me up, unless I take a pain reliever.
It may be something as simple as having a body part "go to sleep". You know, the feeling of numbness, when you have inadvertently cut off circulation to an arm or leg by putting weight on it for a while, followed by tingling when sensation returns. My 21-year-old cat frequently has difficulty moving one hind leg when she first wakes up and shakes the whole leg. I have found that a little gentle message helps speed up the restoration of circulation and normal function.
Perhaps the dog has a form of doggie Alzheimer's. I believe I have seen something like this in my 21-year-old cat, similar to the symptoms my 91-year-old grandfather had. She wakes up and meows, as if she is disoriented and does not know where she is. As soon as I go to her and pet her and she sees where she is, then she settles down. It can be as simple as falling asleep on the couch and waking up facing the back of the couch, instead of where she can see the room. She generally moves around within a small area. If I carry her around with me and go too far from the living room for too long, she gets upset, like she thinks I am getting us lost, and won't be able to find our way back. I moved a litter box a few feet once. She kept going to the spot where it used to be and looking. I finally figured she was either unable to find the new one or unwilling to go in anything but the same old familiar location, so I put it back, and she used it immediately. I have learned not to change the location of anything or vary the routine even slightly and she seems perfectly happy.
Perhaps the dog has obstructive sleep apnea and wakes up gasping for air. I have that. It can be frightening enough when you know what it is. Imagine if it happens to a dog and they don't understand why. It can make you dread going back to sleep if you know you are going to stop breathing while you sleep and wake up gasping for air again. For people, sleeping on your side helps and you can put something behind your back to keep you from rolling over. I don't know if that helps for dogs.
Does the dog have overactive bladder and wake up whining for someone to let him out so he can go? Does he have a doggie door to the outdoors or some paper he is trained to pee on available?
Maybe the dog is having nightmares.
It could be some combination of problems.
If the dog does not sleep right next to the owner or with another dog, in addition to the idea of putting a piece of clothing with the owner's scent on it in the dog bed, you can also try putting a ticking clock or watch, wrapped inside something soft, like a towel, in the bed. I have been told that it simulates the ticking heart of a companion.