When faced with a sudden encounter, most people react without thinking in one of several different ways. To elaborate, if a Bad Guy suddenly decides he wants to beat a person up, that person may automatically:
1) Throw him/herself at the attacker and fight him.
2) Attempt to run away or duck into a ball.
3) Freeze like a deer caught in headlights.
These are not - as Jun implied by putting 'instincts' in single quotes - true instincts; in other words, they're not hard-wired into the Human brain. They are learned responses, picked up from our environment as we grow up. I personally have a hunch, based on my own experience, that the third possibility; 'freeze', is a result of having no real learned response - the body freezes in place while the brain tries to sort out the new situation.
Hope that answers your question.