I'm not a health expert but I've always chalked it up to anxiety. I pretty much woke up that way all of last year. It was exhausting as heck. I noticed that it would be particularly bad whenever I went to bed even slightly anxious (I was anxious all the time last year, so it was quite often), so I started meditating. And honestly? It helped a bit. I still wake up that way from time to time (it's horrible, isn't it? And you end up feeling like you haven't slept at all, which sucks. What sucks more is that the feeling of fear/anxiousness you woke up with seems to cling to you even when you're up and running...), but, like I said, it's usually when I went to bed feeling anxious. Even a little bit.