I got spotted through the ceiling a few times; don't think that's what is going on in your vid though (all kills register unnoticed, don't they?).
I was having 'noticed' problems on 'Les Impardonnables' yesterday. Now, I'm sure I've killed this guy at the window in dozens of other contracts, either by poison, push, or with a pistol; here, however, all those methods would result in losing the no noticed kill bonus.
As in the clip, I've even waited until he's moved to get cover, and the bald guy opposite is still spotting me through the wall.
If I go from the attic start and trigger the conversation, or lure him further into the attic behind the crates, it'll be unnoticed. All this adds about 15-20 seconds to the run I wanted though.