Make sure you aren't a NOT close range. You have to be somewhat mid range in order for it to count. I had same issue as you are describing except I figured it out around the 16 hour mark.
Also, I've tried to do a side quest entirely stealth and I am afraid it's not possible. Because there are some rooms with 4 to 6 guys + turrets and the objective you need to take, steal, hack or kill is in that 1 room. Even if you shoot someone from a perfect angle in a different room and you manage to stay hidden, they all start running like ants and you have to wait forever for the meter to go back into hidden when it's on caution.
Is there no way to attract or bait a individual guard and trick them to follow you into a room?