Ghost / Smooth operator bug?

[desertfoxg]

I'm trying to do a foxiest of the hounds run through. For the police station, I snuck in from the third floor fire escape, went down to the morgue, and grabbed the chip, all without being seen or taking anyone out. Didn't cause any alarms, and was not seen by anyone other than the quest NPC, and didn't get ghost or smooth operator bonuses. I looked on youtube, and there's walkthrough videos where people have gotten the bonuses for doing the same thing I did. What's up? What am I doing wrong? this is on deus ex difficulty

also for the first mission (the sarif factory) I got the ghost bonus for the first "step" of the mission, but on the second step, I only knocked out two guys and hid them where there weren't any other patrols, and never even caused an alarm or caused a camera to become suspicious, and did not receive ghost bonus. Is there something Im missing?