"wakes up partially and almost freaks out, she tries to get as far from me as possible in the bed."
I would be ridiculously concerned by that. That is not normal behavior. My mother used to do stuff similar to that, and she was sexually and physically abused by her father. He was in WWI and WWII and went crazy as a result. She used to have to hide under her bed at night because he would go around with a knife thinking she and the other kids were the enemy and try to stab them.
Does she do that often or just once or twice since you two have been together? I guess anyone could be scared once or twice by a bad dream, but if it is often, I would be concerned.
"Recollect me darlin, raise me to your lips, two undernourished egos, four rotating hips"