that happened to my kitten recently too, it was quite scary! almost seemed like she'd seen or heard something we hadn't. Bizarrely soon after that we bought a new bed frame, our old one broke some months back (no it was nothing like that!) and we'd been sleeping on the mattress which had been moved into a different position, facing the door. She'd been uneasy for a lot of this time. Once we got the new frame and moved the bed into a different position, she's been fine, sleeping well and no scared moments. Couldn't help wondering if it was feng-shui!
You could try a few drops of Rescue Remedy in his water if he's really shocked and scared, to help calm and soothe him. If he won't drink, just rub a little onto his lips. Another one that may help is Aspen, for fear and anxiety with no known cause or Rock Rose for terror.
Hope he's feeling better now