This videos shows four different techniques to use the emetic syringe on the bodyguard located on the balcony outside the auction in Paris. I don't usually play with minimap, but I put it on to show that compromised momentarily appears then disappears. Don't worry about it. This is quite normal and it will not effect your SA rating. If it does remain for you, then I suggest that you do not move until it disappears. For a second or two after using the syringe you can be spotted by him (white dot over his head), and if you move too early it might compromise you.
However, on occasion, as you mentioned, it will glitch and he will not go anywhere. I show two examples at the end. As far as I know this only happens with method two.
By the way, I sent a PM to you and @Watson the other day. Perhaps you each thought the other replied. Neither of you did.