This has happened a number of times. I just had an epic battle with all these people, and were wondering why it seemed I wasn't killing anyone. Turns out, i can hurt them enough that they SHOULD die, but they just get on their knees as if they were giving up, but it won't let me kill them.

The only reason this will happen is if you're trying to kill NPCs who are directly tied to the main quest.

Fortunately, they seem fairly forgiving.