I didn't see this in the Q&A, but it has been hinted at in the thread.

Q. I killed the enemie I needed to kill but they didn't count towards my book. What's happening?

A. The simple answer is you didn't kill the right enemy. The right enemy has a little gear-like symbol above their head. Additionally, if it was the correct enemy, then you didn't have your atma equipped. As an additional point on this, if there is more than one person going for the kill, whoever gets the initial hit on the enemy, will always get the kill count. The other person just needs to get enough hits for it to count for them, too.